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diff --git a/web/dbdoc/IBR_M_0606_R.html b/web/dbdoc/IBR_M_0606_R.html new file mode 100755 index 00000000..a0b507e4 --- /dev/null +++ b/web/dbdoc/IBR_M_0606_R.html @@ -0,0 +1,466 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> +<HTML><HEAD><TITLE>INIA Brain mRNA M430 (June06) RMA</TITLE> +<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> +<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'> +<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'> +<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT> +</HEAD> +<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff> +<TABLE cellSpacing=5 cellPadding=4 width="100%" border=0> +<TBODY> +<TR> +<script language="JavaScript" src="/javascript/header.js"></script> +</TR> +<TR> +<TD bgColor=#eeeeee class="solidBorder"> +<Table width= "100%" cellSpacing=0 cellPadding=5><TR> +<!-- Body Start from Here --> + +<TD vAlign=top width="100%" height=200 bgColor=#eeeeee> +<P class="title">INIA Brain mRNA M430 (June06) RMA <A HREF="/webqtl/main.py?FormID=editHtml"> +<img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A><BR><BR>Accession number: <A HREF="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=113">GN113</A></P> + +<P class="subtitle"> Summary:</P> + + +<Blockquote> +<P> +This June 2006 data freeze provides estimates of mRNA expression in adult forebrain and midbrain from 43 lines of mice including C57BL/6J, DBA/2J, reciprocal F1 hybrids, and 39 BXD recombinant inbred strains. No error terms are providing in this data set. Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (<a href="http://www.iniastress.org" target="_blank" class="fs14">INIA</a>). Samples were hybridized in small pools (<I>n</I> = 3) to a total of 121 Affymetrix M430A and B array pairs. This data set only includes the highest quality subset of 76 arrays that have been quantile normalized at both probe and probe set levels. This data set was initially processed using the <a href="http://stat-www.berkeley.edu/users/bolstad/RMAExpress/RMAExpress.html" target="_blank" class="fs14">RMA</a> protocol. Data were renormalized by Chesler and colleagues at ORNL. A total of 310 probe sets have an LRS values above 50. +</P> +</Blockquote> + + +<P class="subtitle"> About the cases used to generate this set of data:</P> + +<Blockquote> +We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 2 million B vs D SNPs from <a href="http://www.celeradiscoverysystem.com/index.cfm" target="_blank" class="fs14">Celera</a>. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory. BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. <a href="http://www.biomedcentral.com/1471-2156/5/7" target="_blank" class="fs14">2004</a>). Many of the 50 new BXD strains are available from <A HREF="mailto:lulu@nb.utmem.EDU" target="_blank" class="fs14">Lu Lu</A> and colleagues</P> + +<P> All stock was obtained originally from The Jackson Laboratory between 1999 and 2003. Most BXD animals were born and housed at the University of Tennessee Health Science Center. Some cases were bred at the University of Memphis (Douglas Matthews) or the University of Alabama (John Mountz and Hui-Chen Hsu). +</P></Blockquote> + + +<P class="subtitle"> About the tissue used to generate this set of data:</P> + +<Blockquote>The <a href="http://www.iniastress.org" target="_blank" class="fs14">INIA</a> M430 brain Database (Jan06) consists of 78 Affymetrix 430A and 430B microarray pairs. Each pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb or retina, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter, Shirlean Goodwin, and colleagues at the University of Memphis. + +<P><B>Replication and Sample Balance:</B> Our goal was to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. While we achieved this goal technically, not all of the replicates were of sufficient quality to be included in this highly selected set. This data set is now complete and includes more than 20 replicates. Despite the lack of replicates for about 20 strains we still recommend this data set strongly over earliers data sets that included more arrays, many of which are suboptimal. + +<P><B>Batch Structure:</B> Before running the first batch of 30 pairs of array (dated Jan04), we ran four test samples (Nov03). The main batch of 30 includes the four test samples (four technical replicates). The Nov03 data was combined with the Jan04 data and was treated as a single batch that consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. The second large batch was run February 2005 (Feb05) and consists of 71 pairs of arrays. Two more batches were run; the final in December 2005 (16 arrays pairs). Batch effects were corrected at the individual probe level as described below. + + +<P>The table below summarizes information on strain, sex, age, sample name, batch result date, the grouping to which an arrays data set belongs based on expression similarity, and source of mice. + +</Blockquote> +<Blockquote> +<table border="0" cellpadding="0" cellspacing="0" bgcolor="#000000" width="75%" align="Center"> +<tr> +<td> +<table width="100%" border="0" cellpadding="7" cellspacing="1"> +<tr bgcolor="royalblue"><td><font color=#FFFFFF>Id</font></td><td><font color=#FFFFFF>Strain</font></td> +<td><font color=#FFFFFF>Sex</font></td> +<td><font color=#FFFFFF>Age</font></td> +<td><font color=#FFFFFF>Sample</td> +<td><font color=#FFFFFF><center>Batch</center></font></td> +<td><font color=#FFFFFF><center>Final Grouping</center></font></td> +<td><font color=#FFFFFF>Source</font></td></tr> +<tr bgcolor="#eeeeee"><td>1</td><td>B6D2F1</td><td>F</td><td>127</td><td>R0919F1</td><td><center>2</center></td><td><center>e_2</center></td><td>UTM JB</td></tr> +<tr bgcolor="#eeeeee"><td>2</td><td>B6D2F1</td><td>F</td><td>127</td><td>R0919F2</td><td><center>2</center></td><td><center>e_2</center></td><td>UTM JB</td></tr> +<tr bgcolor="#eeeeee"><td>3</td><td>B6D2F1</td><td>F</td><td>64</td><td>R1053F1</td><td><center>3</center></td><td><center>g_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>4</td><td>B6D2F1</td><td>F</td><td>64</td><td>R1053F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>5</td><td>B6D2F1</td><td>M</td><td>66</td><td>R1057F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>6</td><td>D2B6F1</td><td>F</td><td>57</td><td>R1066F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>7</td><td>C57BL/6J</td><td>F</td><td>65</td><td>R0903F1</td><td><center>1</center></td><td><center>se_1</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>8</td><td>C57BL/6J</td><td>F</td><td>65</td><td>R0903F1</td><td><center>2</center></td><td><center>e_2</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>9</td><td>C57BL/6J</td><td>M</td><td>66</td><td>R0906F1</td><td><center>1</center></td><td><center>e_1</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>10</td><td>C57BL/6J</td><td>M</td><td>76</td><td>R0997F1</td><td><center>3</center></td><td><center>g_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>11</td><td>DBA/2J</td><td>F</td><td>60</td><td>R0917F1</td><td><center>1</center></td><td><center>e_1</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>12</td><td>DBA/2J</td><td>F</td><td>64</td><td>R1123F1</td><td><center>3</center></td><td><center>g_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>13</td><td>DBA/2J</td><td>M</td><td>60</td><td>R0918F1</td><td><center>2</center></td><td><center>sgA_2</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>14</td><td>DBA/2J</td><td>M</td><td>73</td><td>R1009F1</td><td><center>3</center></td><td><center>w_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>15</td><td>BXD1</td><td>M</td><td>181</td><td>R0956F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM JB</td></tr> +<tr bgcolor="#eeeeee"><td>16</td><td>BXD2</td><td>F</td><td>142</td><td>R0907F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UAB</td></tr> +<tr bgcolor="#eeeeee"><td>17</td><td>BXD5</td><td>F</td><td>56</td><td>R0744F1</td><td><center>3</center></td><td><center>o_3</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>18</td><td>BXD5</td><td>M</td><td>71</td><td>R0728F1</td><td><center>2</center></td><td><center>e_2</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>19</td><td>BXD6</td><td>F</td><td>57</td><td>R1711F1</td><td><center>3</center></td><td><center>g_3</center></td><td>JAX</td></tr> +<tr bgcolor="#eeeeee"><td>20</td><td>BXD8</td><td>M</td><td>71</td><td>R2664F1</td><td><center>4</center></td><td><center>se_4</center></td><td>JAX</td></tr> +<tr bgcolor="#eeeeee"><td>21</td><td>BXD11</td><td>F</td><td>97</td><td>R0745F1</td><td><center>3</center></td><td><center>gA_3</center></td><td>UAB</td></tr> +<tr bgcolor="#eeeeee"><td>22</td><td>BXD12</td><td>F</td><td>64</td><td>R0896F1</td><td><center>3</center></td><td><center>o_3</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>23</td><td>BXD12</td><td>M</td><td>64</td><td>R0897F1</td><td><center>2</center></td><td><center>e_2</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>24</td><td>BXD13</td><td>F</td><td>86</td><td>R0748F1</td><td><center>2</center></td><td><center>e_2</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>25</td><td>BXD13</td><td>F</td><td>86</td><td>R0730F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>26</td><td>BXD13</td><td>M</td><td>76</td><td>R0929F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>27</td><td>BXD14</td><td>M</td><td>68</td><td>R1051F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>28</td><td>BXD15</td><td>F</td><td>80</td><td>R0928F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>29</td><td>BXD18</td><td>F</td><td>108</td><td>R0771F1</td><td><center>2</center></td><td><center>e_2</center></td><td>UAB</td></tr> +<tr bgcolor="#eeeeee"><td>30</td><td>BXD19</td><td>M</td><td>157</td><td>R1229F1</td><td><center>3</center></td><td><center>gA_3</center></td><td>UTM JB</td></tr> +<tr bgcolor="#eeeeee"><td>31</td><td>BXD21</td><td>F</td><td>67</td><td>R0740F1</td><td><center>3</center></td><td><center>gA_3</center></td><td>UAB</td></tr> +<tr bgcolor="#eeeeee"><td>32</td><td>BXD23</td><td>F</td><td>88</td><td>R0815F1</td><td><center>3</center></td><td><center>gA_3</center></td><td>UAB</td></tr> +<tr bgcolor="#eeeeee"><td>33</td><td>BXD23</td><td>F</td><td>66</td><td>R1035F1</td><td><center>3</center></td><td><center>gA_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>34</td><td>BXD23</td><td>M</td><td>66</td><td>R1256F1</td><td><center>4</center></td><td><center>e_4</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>35</td><td>BXD23</td><td>M</td><td>66</td><td>R1037F1</td><td><center>3</center></td><td><center>gA_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>36</td><td>BXD24</td><td>F</td><td>71</td><td>R0914F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>37</td><td>BXD24</td><td>M</td><td>71</td><td>R0913F1</td><td><center>2</center></td><td><center>e_2</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>38</td><td>BXD25</td><td>F</td><td>74</td><td>R0373F1</td><td><center>2</center></td><td><center>e_2</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>39</td><td>BXD25</td><td>M</td><td>58</td><td>R2623F1</td><td><center>4</center></td><td><center>e_4</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>40</td><td>BXD27</td><td>M</td><td>54</td><td>R2660F1</td><td><center>4</center></td><td><center>e_4</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>41</td><td>BXD28</td><td>F</td><td>113</td><td>R0892F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>42</td><td>BXD28</td><td>M</td><td>79</td><td>R0911F1</td><td><center>3</center></td><td><center>g_3</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>43</td><td>BXD31</td><td>M</td><td>61</td><td>R1141F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>44</td><td>BXD32</td><td>F</td><td>93</td><td>R0898F1</td><td><center>2</center></td><td><center>e_2</center></td><td>UAB</td></tr> +<!---<tr bgcolor="#eeeeee"><td>45</td><td>BXD32</td><td>F</td><td>76</td><td>R1214F1</td><td><center>3</center></td><td><center>w_3</center></td><td>UMemphis</td></tr>---> +<tr bgcolor="#eeeeee"><td>46</td><td>BXD32</td><td>M</td><td>76</td><td>R1217F2</td><td><center>4</center></td><td><center>e_4</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>47</td><td>BXD32</td><td>M</td><td>65</td><td>R1478F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>48</td><td>BXD34</td><td>M</td><td>72</td><td>R0916F1</td><td><center>2</center></td><td><center>e_2</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>49</td><td>BXD34</td><td>F</td><td>92</td><td>R0900F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>50</td><td>BXD36</td><td>F</td><td>79</td><td>R2654F1</td><td><center>4</center></td><td><center>e_4</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>51</td><td>BXD36</td><td>F</td><td>61</td><td>R1145F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>52</td><td>BXD36</td><td>M</td><td>77</td><td>R0926F1</td><td><center>2</center></td><td><center>e_2</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>53</td><td>BXD38</td><td>F</td><td>69</td><td>R0729F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>54</td><td>BXD38</td><td>F</td><td>83</td><td>R1208F1</td><td><center>3</center></td><td><center>g_3</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>55</td><td>BXD39</td><td>F</td><td>76</td><td>R1712F1</td><td><center>3</center></td><td><center>e_3</center></td><td>JAX</td></tr> +<!---<tr bgcolor="#eeeeee"><td>56</td><td>BXD39</td><td>M</td><td>71</td><td>R0602F1</td><td><center>3</center></td><td><center>w_3</center></td><td>UAB</td></tr>--> +<tr bgcolor="#eeeeee"><td>57</td><td>BXD40</td><td>F</td><td>184</td><td>R0741F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UAB</td></tr> +<tr bgcolor="#eeeeee"><td>58</td><td>BXD40</td><td>M</td><td>56</td><td>R0894F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UMemphis</td></tr> +<tr bgcolor="#eeeeee"><td>59</td><td>BXD42</td><td>F</td><td>100</td><td>R0742F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UAB</td></tr> +<tr bgcolor="#eeeeee"><td>60</td><td>BXD43</td><td>F</td><td>61</td><td>R1199F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>61</td><td>BXD43</td><td>F</td><td>59</td><td>R0980F1</td><td><center>4</center></td><td><center>e_4</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>62</td><td>BXD44</td><td>M</td><td>58</td><td>R1072F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>63</td><td>BXD45</td><td>F</td><td>58</td><td>R1398F1</td><td><center>3</center></td><td><center>o_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>64</td><td>BXD45</td><td>M</td><td>81</td><td>R1658F2</td><td><center>4</center></td><td><center>e_4</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>65</td><td>BXD48</td><td>F</td><td>59</td><td>R0946F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>66</td><td>BXD51</td><td>F</td><td>63</td><td>R1430F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>67</td><td>BXD51</td><td>M</td><td>65</td><td>R1001F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>68</td><td>BXD60</td><td>M</td><td>59</td><td>R1075F1</td><td><center>3</center></td><td><center>g_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>69</td><td>BXD62</td><td>M</td><td>58</td><td>R1027F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>70</td><td>BXD69</td><td>F</td><td>60</td><td>R1438F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>71</td><td>BXD69</td><td>M</td><td>64</td><td>R1193F1</td><td><center>3</center></td><td><center>o_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>72</td><td>BXD73</td><td>F</td><td>60</td><td>R1275F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>73</td><td>BXD73</td><td>M</td><td>76</td><td>R1442F1</td><td><center>3</center></td><td><center>g_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>74</td><td>BXD77</td><td>M</td><td>61</td><td>R1426F1</td><td><center>3</center></td><td><center>g_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>75</td><td>BXD87</td><td>F</td><td>89</td><td>R1713F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>76</td><td>BXD90</td><td>F</td><td>71</td><td>R2628F1</td><td><center>4</center></td><td><center>e_4</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>77</td><td>BXD90</td><td>M</td><td>61</td><td>R1452F</td><td><center>3</center></td><td><center>g_3</center></td><td>UTM RW</td></tr> +<tr bgcolor="#eeeeee"><td>78</td><td>BXD92</td><td>F</td><td>58</td><td>R1299F1</td><td><center>3</center></td><td><center>e_3</center></td><td>UTM RW</td></tr> </table> +</td> +</tr> +</table> + +<P>The table below quality information on scale factor, background, present, absent, marginal, and control genes to which an arrays data set is from it's report file. +</Blockquote> +<Blockquote> +<table border="0" cellpadding="0" cellspacing="0" bgcolor="#000000" width="75%" align="Center"> +<tr> +<td> +<table width="100%" border="0" cellpadding="7" cellspacing="1"> +<tr bgcolor="royalblue"><td><font color=#FFFFFF>Id</font></td><td><font color=#FFFFFF>Strain</font></td> +<td><font color=#FFFFFF>Sample</td> +<td><font color=#FFFFFF><center>Final grouping</center></font></td> +<td><font color=#FFFFFF><center>Set</center></font></td> +<td><font color=#FFFFFF>scale factor</font></td> +<td><font color=#FFFFFF>back ground</font></td> +<td><font color=#FFFFFF><center>present</center></font></td> +<td><font color=#FFFFFF>absent</font></td> +<td><font color=#FFFFFF>marginal</font></td> +<td><font color=#FFFFFF>Affy- b- Actin</font></td> +<td><font color=#FFFFFF>Affy- Gapdh</font></td> +</tr> +<tr bgcolor="#eeeeee"><td>1</td><td>B6D2F1</td><td>R0919F1</td><td>e_B2</td><td><center>A</center></td><td>14.212</td><td>46.93</td><td>0.417</td><td>0.564</td><td>0.019</td><td>1.24</td><td>0.8</td></tr> +<tr bgcolor="#eeeeee"><td>1</td><td>B6D2F1</td><td>R0919F1</td><td>e_B2</td><td><center>B</center></td><td>30.349</td><td>42.21</td><td>0.233</td><td>0.748</td><td>0.019</td><td>1.24</td><td>0.74</td></tr> +<tr bgcolor="#eeeeee"><td>2</td><td>B6D2F1</td><td>R0919F2</td><td>e_B2</td><td><center>A</center></td><td>5.95</td><td>53</td><td>0.468</td><td>0.511</td><td>0.021</td><td>1.17</td><td>0.73</td></tr> +<tr bgcolor="#eeeeee"><td>2</td><td>B6D2F1</td><td>R0919F2</td><td>e_B2</td><td><center>B</center></td><td>14.795</td><td>47.95</td><td>0.264</td><td>0.716</td><td>0.02</td><td>1.19</td><td>0.75</td></tr> +<tr bgcolor="#eeeeee"><td>3</td><td>B6D2F1</td><td>R1053F1</td><td>g_B3</td><td><center>A</center></td><td>4.445</td><td>50.82</td><td>0.536</td><td>0.447</td><td>0.017</td><td>1.92</td><td>1.69</td></tr> +<tr bgcolor="#eeeeee"><td>3</td><td>B6D2F1</td><td>R1053F1</td><td>g_B3</td><td><center>B</center></td><td>16.596</td><td>51.44</td><td>0.278</td><td>0.702</td><td>0.02</td><td>1.93</td><td>1.76</td></tr> +<tr bgcolor="#eeeeee"><td>4</td><td>B6D2F1</td><td>R1053F1</td><td>e_B3</td><td><center>A</center></td><td>11.196</td><td>42.4</td><td>0.457</td><td>0.523</td><td>0.02</td><td>1.84</td><td>1.32</td></tr> +<tr bgcolor="#eeeeee"><td>4</td><td>B6D2F1</td><td>R1053F1</td><td>e_B3</td><td><center>B</center></td><td>16.596</td><td>51.44</td><td>0.278</td><td>0.702</td><td>0.02</td><td>1.93</td><td>1.76</td></tr> +<tr bgcolor="#eeeeee"><td>5</td><td>B6D2F1</td><td>R1057F1</td><td>e_B3</td><td><center>A</center></td><td>7.332</td><td>42.21</td><td>0.505</td><td>0.475</td><td>0.02</td><td>1.64</td><td>1.2</td></tr> +<tr bgcolor="#eeeeee"><td>5</td><td>B6D2F1</td><td>R1057F1</td><td>e_B3</td><td><center>B</center></td><td>16.444</td><td>40.31</td><td>0.314</td><td>0.661</td><td>0.025</td><td>1.13</td><td>1.31</td></tr> +<tr bgcolor="#eeeeee"><td>6</td><td>C57BL/6J</td><td>R0903F1</td><td>se_B1</td><td><center>A</center></td><td>10.15</td><td>46.46</td><td>0.418</td><td>0.562</td><td>0.019</td><td>1.13</td><td>0.76</td></tr> +<tr bgcolor="#eeeeee"><td>6</td><td>C57BL/6J</td><td>R0903F1</td><td>se_B1</td><td><center>B</center></td><td>20.223</td><td>47.78</td><td>0.222</td><td>0.759</td><td>0.018</td><td>1.36</td><td>0.89</td></tr> +<tr bgcolor="#eeeeee"><td>7</td><td>C57BL/6J</td><td>R0903F1</td><td>e_B2</td><td><center>A</center></td><td>7.406</td><td>52.47</td><td>0.473</td><td>0.507</td><td>0.02</td><td>1.01</td><td>0.74</td></tr> +<tr bgcolor="#eeeeee"><td>7</td><td>C57BL/6J</td><td>R0903F1</td><td>e_B2</td><td><center>B</center></td><td>20.71</td><td>46.98</td><td>0.252</td><td>0.729</td><td>0.02</td><td>1.08</td><td>0.74</td></tr> +<tr bgcolor="#eeeeee"><td>8</td><td>C57BL/6J</td><td>R0906F1</td><td>e_B1</td><td><center>A</center></td><td>9.407</td><td>46.55</td><td>0.439</td><td>0.54</td><td>0.022</td><td>1</td><td>0.8</td></tr> +<tr bgcolor="#eeeeee"><td>8</td><td>C57BL/6J</td><td>R0906F1</td><td>e_B1</td><td><center>B</center></td><td>28.77</td><td>44.52</td><td>0.21</td><td>0.77</td><td>0.019</td><td>1.04</td><td>0.74</td></tr> +<tr bgcolor="#eeeeee"><td>9</td><td>C57BL/6J</td><td>R0997F1</td><td>g_B3</td><td><center>A</center></td><td>8.118</td><td>55.74</td><td>0.448</td><td>0.53</td><td>0.022</td><td>0.9</td><td>1.04</td></tr> +<tr bgcolor="#eeeeee"><td>9</td><td>C57BL/6J</td><td>R0997F1</td><td>g_B3</td><td><center>B</center></td><td>13.24</td><td>49.64</td><td>0.316</td><td>0.661</td><td>0.023</td><td>1.41</td><td>1.11</td></tr> +<tr bgcolor="#eeeeee"><td>10</td><td>D2B6F1</td><td>R1066F1</td><td>e_B3</td><td><center>A</center></td><td>8.147</td><td>46.39</td><td>0.481</td><td>0.5</td><td>0.019</td><td>0.97</td><td>1.22</td></tr> +<tr bgcolor="#eeeeee"><td>10</td><td>D2B6F1</td><td>R1066F1</td><td>e_B3</td><td><center>B</center></td><td>18.835</td><td>43.24</td><td>0.285</td><td>0.695</td><td>0.021</td><td>1.11</td><td>1.29</td></tr> +<tr bgcolor="#eeeeee"><td>11</td><td>DBA/2J</td><td>R0917F1</td><td>e_B1</td><td><center>A</center></td><td>13.775</td><td>50.2</td><td>0.253</td><td>0.729</td><td>0.019</td><td>1.18</td><td>0.76</td></tr> +<tr bgcolor="#eeeeee"><td>11</td><td>DBA/2J</td><td>R0917F1</td><td>e_B1</td><td><center>B</center></td><td>22.301</td><td>47.49</td><td>0.241</td><td>0.741</td><td>0.018</td><td>1.37</td><td>0.88</td></tr> +<tr bgcolor="#eeeeee"><td>12</td><td>DBA/2J</td><td>R1123F1</td><td>g_B3</td><td><center>A</center></td><td>9.452</td><td>50.14</td><td>0.456</td><td>0.523</td><td>0.021</td><td>1.37</td><td>1.87</td></tr> +<tr bgcolor="#eeeeee"><td>12</td><td>DBA/2J</td><td>R1123F1</td><td>g_B3</td><td><center>B</center></td><td>23.467</td><td>42.27</td><td>0.25</td><td>0.729</td><td>0.021</td><td>0.91</td><td>1.9</td></tr> +<tr bgcolor="#eeeeee"><td>13</td><td>DBA/2J</td><td>R0918F1</td><td>sgA_B2</td><td><center>A</center></td><td>9.105</td><td>48.24</td><td>0.462</td><td>0.517</td><td>0.019</td><td>1.22</td><td>0.81</td></tr> +<tr bgcolor="#eeeeee"><td>13</td><td>DBA/2J</td><td>R0918F1</td><td>sgA_B2</td><td><center>B</center></td><td>25.007</td><td>46.99</td><td>0.244</td><td>0.736</td><td>0.019</td><td>1.22</td><td>0.81</td></tr> +<tr bgcolor="#eeeeee"><td>14</td><td>DBA/2J</td><td>R1009F1</td><td>w_B3</td><td><center>A</center></td><td>5.736</td><td>42.88</td><td>0.527</td><td>0.455</td><td>0.017</td><td>1.11</td><td>2.4</td></tr> +<tr bgcolor="#eeeeee"><td>14</td><td>DBA/2J</td><td>R1009F1</td><td>w_B3</td><td><center>B</center></td><td>17.739</td><td>43.75</td><td>0.291</td><td>0.69</td><td>0.019</td><td>0.91</td><td>2.36</td></tr> +<tr bgcolor="#eeeeee"><td>15</td><td>BXD1</td><td>R0956F1</td><td>e_B3</td><td><center>A</center></td><td>4.923</td><td>44.74</td><td>0.519</td><td>0.46</td><td>0.021</td><td>1.5</td><td>1.09</td></tr> +<tr bgcolor="#eeeeee"><td>15</td><td>BXD1</td><td>R0956F1</td><td>e_B3</td><td><center>B</center></td><td>15.937</td><td>39.5</td><td>0.31</td><td>0.665</td><td>0.025</td><td>1.47</td><td>1.21</td></tr> +<tr bgcolor="#eeeeee"><td>16</td><td>BXD2</td><td>R0907F1</td><td>e_B3</td><td><center>A</center></td><td>6.191</td><td>45.77</td><td>0.48</td><td>0.498</td><td>0.022</td><td>1.37</td><td>1.23</td></tr> +<tr bgcolor="#eeeeee"><td>16</td><td>BXD2</td><td>R0907F1</td><td>e_B3</td><td><center>B</center></td><td>16.15</td><td>43.78</td><td>0.3</td><td>0.677</td><td>0.023</td><td>1.74</td><td>1.37</td></tr> +<tr bgcolor="#eeeeee"><td>17</td><td>BXD5</td><td>R0744F1</td><td>o_B3</td><td><center>A</center></td><td>10.448</td><td>60.78</td><td>0.403</td><td>0.576</td><td>0.021</td><td>1.23</td><td>1.38</td></tr> +<tr bgcolor="#eeeeee"><td>17</td><td>BXD5</td><td>R0744F1</td><td>o_B3</td><td><center>B</center></td><td>28.054</td><td>44.72</td><td>0.236</td><td>0.746</td><td>0.018</td><td>1.43</td><td>1.68</td></tr> +<tr bgcolor="#eeeeee"><td>18</td><td>BXD5</td><td>R0728F1</td><td>e_B2</td><td><center>A</center></td><td>7.884</td><td>53.56</td><td>0.43</td><td>0.549</td><td>0.021</td><td>1.12</td><td>0.71</td></tr> +<tr bgcolor="#eeeeee"><td>18</td><td>BXD5</td><td>R0728F1</td><td>e_B2</td><td><center>B</center></td><td>18.92</td><td>42.5</td><td>0.245</td><td>0.735</td><td>0.019</td><td>1</td><td>0.76</td></tr> +<tr bgcolor="#eeeeee"><td>19</td><td>BXD6</td><td>R1711F1</td><td>g_B3</td><td><center>A</center></td><td>7.1</td><td>46.57</td><td>0.498</td><td>0.481</td><td>0.02</td><td>1.97</td><td>1.66</td></tr> +<tr bgcolor="#eeeeee"><td>19</td><td>BXD6</td><td>R1711F1</td><td>g_B3</td><td><center>B</center></td><td>12.465</td><td>46.02</td><td>0.319</td><td>0.66</td><td>0.022</td><td>2.06</td><td>1.78</td></tr> +<tr bgcolor="#eeeeee"><td>20</td><td>BXD8</td><td>R2664F1</td><td>se_B4</td><td><center>A</center></td><td>2.126</td><td>45.64</td><td>0.594</td><td>0.39</td><td>0.016</td><td>1.73</td><td>1</td></tr> +<tr bgcolor="#eeeeee"><td>20</td><td>BXD8</td><td>R2664F1</td><td>se_B4</td><td><center>B</center></td><td>7.133</td><td>41.85</td><td>0.377</td><td>0.603</td><td>0.02</td><td>1.95</td><td>0.99</td></tr> +<tr bgcolor="#eeeeee"><td>21</td><td>BXD11</td><td>R0745F1</td><td>gA_B3</td><td><center>A</center></td><td>6.242</td><td>40.99</td><td>0.501</td><td>0.48</td><td>0.019</td><td>1.4</td><td>1.24</td></tr> +<tr bgcolor="#eeeeee"><td>21</td><td>BXD11</td><td>R0745F1</td><td>gA_B3</td><td><center>B</center></td><td>18.681</td><td>41.11</td><td>0.278</td><td>0.702</td><td>0.02</td><td>1.28</td><td>1.27</td></tr> +<tr bgcolor="#eeeeee"><td>22</td><td>BXD12</td><td>R0896F1</td><td>o_B3</td><td><center>A</center></td><td>8.237</td><td>51.23</td><td>0.433</td><td>0.546</td><td>0.021</td><td>1.72</td><td>1.28</td></tr> +<tr bgcolor="#eeeeee"><td>22</td><td>BXD12</td><td>R0896F1</td><td>o_B3</td><td><center>B</center></td><td>19.781</td><td>43.61</td><td>0.264</td><td>0.714</td><td>0.022</td><td>1.44</td><td>1.45</td></tr> +<tr bgcolor="#eeeeee"><td>23</td><td>BXD12</td><td>R0897F1</td><td>e_B2</td><td><center>A</center></td><td>10.713</td><td>46.56</td><td>0.421</td><td>0.56</td><td>0.019</td><td>1.23</td><td>0.75</td></tr> +<tr bgcolor="#eeeeee"><td>23</td><td>BXD12</td><td>R0897F1</td><td>e_B2</td><td><center>B</center></td><td>20.093</td><td>50.31</td><td>0.236</td><td>0.744</td><td>0.02</td><td>1.25</td><td>0.76</td></tr> +<tr bgcolor="#eeeeee"><td>24</td><td>BXD13</td><td>R0748F1</td><td>e_B2</td><td><center>A</center></td><td>7.149</td><td>57.35</td><td>0.435</td><td>0.543</td><td>0.022</td><td>1.02</td><td>0.74</td></tr> +<tr bgcolor="#eeeeee"><td>24</td><td>BXD13</td><td>R0748F1</td><td>e_B2</td><td><center>B</center></td><td>12.77</td><td>56.44</td><td>0.248</td><td>0.734</td><td>0.019</td><td>1.05</td><td>0.8</td></tr> +<tr bgcolor="#eeeeee"><td>25</td><td>BXD13</td><td>R0730F1</td><td>e_B3</td><td><center>A</center></td><td>6.076</td><td>44.57</td><td>0.49</td><td>0.488</td><td>0.022</td><td>1.26</td><td>1.45</td></tr> +<tr bgcolor="#eeeeee"><td>25</td><td>BXD13</td><td>R0730F1</td><td>e_B3</td><td><center>B</center></td><td>15.7</td><td>44.24</td><td>0.293</td><td>0.687</td><td>0.02</td><td>1.31</td><td>1.52</td></tr> +<tr bgcolor="#eeeeee"><td>26</td><td>BXD13</td><td>R0929F1</td><td>e_B3</td><td><center>A</center></td><td>5.493</td><td>47.46</td><td>0.507</td><td>0.472</td><td>0.021</td><td>1.65</td><td>1.35</td></tr> +<tr bgcolor="#eeeeee"><td>26</td><td>BXD13</td><td>R0929F1</td><td>e_B3</td><td><center>B</center></td><td>14.739</td><td>46.05</td><td>0.301</td><td>0.677</td><td>0.023</td><td>0.93</td><td>1.62</td></tr> +<tr bgcolor="#eeeeee"><td>27</td><td>BXD14</td><td>R1051F1</td><td>e_B3</td><td><center>A</center></td><td>6.393</td><td>45.19</td><td>0.49</td><td>0.489</td><td>0.021</td><td>1.22</td><td>1.26</td></tr> +<tr bgcolor="#eeeeee"><td>27</td><td>BXD14</td><td>R1051F1</td><td>e_B3</td><td><center>B</center></td><td>15.488</td><td>41.14</td><td>0.325</td><td>0.653</td><td>0.022</td><td>1.12</td><td>1.38</td></tr> +<tr bgcolor="#eeeeee"><td>28</td><td>BXD15</td><td>R0928F1</td><td>e_B3</td><td><center>A</center></td><td>5.646</td><td>39.95</td><td>0.524</td><td>0.456</td><td>0.02</td><td>1.95</td><td>1.34</td></tr> +<tr bgcolor="#eeeeee"><td>28</td><td>BXD15</td><td>R0928F1</td><td>e_B3</td><td><center>B</center></td><td>19.344</td><td>37.65</td><td>0.296</td><td>0.682</td><td>0.023</td><td>1.33</td><td>1.42</td></tr> +<tr bgcolor="#eeeeee"><td>29</td><td>BXD18</td><td>R0771F1</td><td>e_B2</td><td><center>A</center></td><td>4.168</td><td>54.8</td><td>0.503</td><td>0.477</td><td>0.02</td><td>1.13</td><td>0.77</td></tr> +<tr bgcolor="#eeeeee"><td>29</td><td>BXD18</td><td>R0771F1</td><td>e_B2</td><td><center>B</center></td><td>9.679</td><td>54.7</td><td>0.277</td><td>0.702</td><td>0.02</td><td>1.4</td><td>0.76</td></tr> +<tr bgcolor="#eeeeee"><td>30</td><td>BXD19</td><td>R1229F1</td><td>gA_B3</td><td><center>A</center></td><td>6.991</td><td>39.65</td><td>0.49</td><td>0.491</td><td>0.02</td><td>1.92</td><td>1.29</td></tr> +<tr bgcolor="#eeeeee"><td>30</td><td>BXD19</td><td>R1229F1</td><td>gA_B3</td><td><center>B</center></td><td>20.945</td><td>40.5</td><td>0.277</td><td>0.702</td><td>0.021</td><td>1.54</td><td>1.22</td></tr> +<tr bgcolor="#eeeeee"><td>31</td><td>BXD21</td><td>R0740F1</td><td>gA_B3</td><td><center>A</center></td><td>6.229</td><td>42.24</td><td>0.483</td><td>0.495</td><td>0.022</td><td>1.31</td><td>1.25</td></tr> +<tr bgcolor="#eeeeee"><td>31</td><td>BXD21</td><td>R0740F1</td><td>gA_B3</td><td><center>B</center></td><td>16.584</td><td>41.88</td><td>0.306</td><td>0.673</td><td>0.021</td><td>1.43</td><td>1.23</td></tr> +<tr bgcolor="#eeeeee"><td>32</td><td>BXD23</td><td>R0815F1</td><td>gA_B3</td><td><center>A</center></td><td>4.753</td><td>48.12</td><td>0.521</td><td>0.46</td><td>0.019</td><td>1.4</td><td>1.06</td></tr> +<tr bgcolor="#eeeeee"><td>32</td><td>BXD23</td><td>R0815F1</td><td>gA_B3</td><td><center>B</center></td><td>11.555</td><td>39.41</td><td>0.353</td><td>0.626</td><td>0.022</td><td>1.44</td><td>1.1</td></tr> +<tr bgcolor="#eeeeee"><td>33</td><td>BXD23</td><td>R1035F1</td><td>gA_B3</td><td><center>A</center></td><td>6.281</td><td>39.58</td><td>0.503</td><td>0.476</td><td>0.02</td><td>1.31</td><td>1.6</td></tr> +<tr bgcolor="#eeeeee"><td>33</td><td>BXD23</td><td>R1035F1</td><td>gA_B3</td><td><center>B</center></td><td>22.536</td><td>34.86</td><td>0.292</td><td>0.686</td><td>0.021</td><td>1.31</td><td>1.67</td></tr> +<tr bgcolor="#eeeeee"><td>34</td><td>BXD23</td><td>R1256F1</td><td>e_B4</td><td><center>A</center></td><td>2.233</td><td>46.66</td><td>0.575</td><td>0.408</td><td>0.017</td><td>1.8</td><td>1.13</td></tr> +<tr bgcolor="#eeeeee"><td>34</td><td>BXD23</td><td>R1256F1</td><td>e_B4</td><td><center>B</center></td><td>4.862</td><td>43.16</td><td>0.399</td><td>0.58</td><td>0.021</td><td>1.73</td><td>1.01</td></tr> +<tr bgcolor="#eeeeee"><td>35</td><td>BXD23</td><td>R1037F1</td><td>gA_B3</td><td><center>A</center></td><td>5.37</td><td>41.47</td><td>0.519</td><td>0.462</td><td>0.019</td><td>1.35</td><td>1.25</td></tr> +<tr bgcolor="#eeeeee"><td>35</td><td>BXD23</td><td>R1037F1</td><td>gA_B3</td><td><center>B</center></td><td>18.483</td><td>37.49</td><td>0.305</td><td>0.671</td><td>0.024</td><td>1.24</td><td>1.28</td></tr> +<tr bgcolor="#eeeeee"><td>36</td><td>BXD24</td><td>R0914F1</td><td>e_B3</td><td><center>A</center></td><td>6.212</td><td>51.11</td><td>0.497</td><td>0.482</td><td>0.021</td><td>1.09</td><td>1.53</td></tr> +<tr bgcolor="#eeeeee"><td>36</td><td>BXD24</td><td>R0914F1</td><td>e_B3</td><td><center>B</center></td><td>19.649</td><td>36.07</td><td>0.309</td><td>0.671</td><td>0.021</td><td>1.4</td><td>1.76</td></tr> +<tr bgcolor="#eeeeee"><td>37</td><td>BXD24</td><td>R0913F1</td><td>e_B2</td><td><center>A</center></td><td>9.002</td><td>49.85</td><td>0.437</td><td>0.543</td><td>0.02</td><td>1.24</td><td>0.71</td></tr> +<tr bgcolor="#eeeeee"><td>37</td><td>BXD24</td><td>R0913F1</td><td>e_B2</td><td><center>B</center></td><td>14.375</td><td>51.49</td><td>0.246</td><td>0.734</td><td>0.02</td><td>1.36</td><td>0.79</td></tr> +<tr bgcolor="#eeeeee"><td>38</td><td>BXD25</td><td>R0373F1</td><td>e_B2</td><td><center>A</center></td><td>6.222</td><td>56.95</td><td>0.457</td><td>0.522</td><td>0.022</td><td>1.37</td><td>0.75</td></tr> +<tr bgcolor="#eeeeee"><td>38</td><td>BXD25</td><td>R0373F1</td><td>e_B2</td><td><center>B</center></td><td>8.337</td><td>50.91</td><td>0.291</td><td>0.685</td><td>0.024</td><td>1.19</td><td>0.77</td></tr> +<tr bgcolor="#eeeeee"><td>39</td><td>BXD25</td><td>R2623F1</td><td>e_B4</td><td><center>A</center></td><td>1.985</td><td>45.8</td><td>0.588</td><td>0.395</td><td>0.016</td><td>1.6</td><td>1</td></tr> +<tr bgcolor="#eeeeee"><td>39</td><td>BXD25</td><td>R2623F1</td><td>e_B4</td><td><center>B</center></td><td>7.555</td><td>40</td><td>0.374</td><td>0.607</td><td>0.019</td><td>1.78</td><td>1.03</td></tr> +<tr bgcolor="#eeeeee"><td>40</td><td>BXD27</td><td>R2660F1</td><td>e_B4</td><td><center>A</center></td><td>2.688</td><td>51.77</td><td>0.582</td><td>0.403</td><td>0.016</td><td>1.4</td><td>0.84</td></tr> +<tr bgcolor="#eeeeee"><td>40</td><td>BXD27</td><td>R2660F1</td><td>e_B4</td><td><center>B</center></td><td>5.735</td><td>54.08</td><td>0.392</td><td>0.588</td><td>0.02</td><td>1.51</td><td>0.78</td></tr> +<tr bgcolor="#eeeeee"><td>41</td><td>BXD28</td><td>R0892F1</td><td>e_B3</td><td><center>A</center></td><td>4.143</td><td>47.2</td><td>0.537</td><td>0.442</td><td>0.021</td><td>1.05</td><td>1.08</td></tr> +<tr bgcolor="#eeeeee"><td>41</td><td>BXD28</td><td>R0892F1</td><td>e_B3</td><td><center>B</center></td><td>16.413</td><td>45.83</td><td>0.297</td><td>0.682</td><td>0.021</td><td>1.04</td><td>1.23</td></tr> +<tr bgcolor="#eeeeee"><td>42</td><td>BXD28</td><td>R0911F1</td><td>g_B3</td><td><center>A</center></td><td>5.811</td><td>43.06</td><td>0.517</td><td>0.465</td><td>0.018</td><td>1.19</td><td>1.43</td></tr> +<tr bgcolor="#eeeeee"><td>42</td><td>BXD28</td><td>R0911F1</td><td>g_B3</td><td><center>B</center></td><td>16.22</td><td>41.15</td><td>0.3</td><td>0.678</td><td>0.022</td><td>0.85</td><td>1.65</td></tr> +<tr bgcolor="#eeeeee"><td>43</td><td>BXD31</td><td>R1141F1</td><td>e_B3</td><td><center>A</center></td><td>3.607</td><td>42.59</td><td>0.547</td><td>0.435</td><td>0.019</td><td>1</td><td>1.15</td></tr> +<tr bgcolor="#eeeeee"><td>43</td><td>BXD31</td><td>R1141F1</td><td>e_B3</td><td><center>B</center></td><td>11.826</td><td>41.26</td><td>0.329</td><td>0.65</td><td>0.021</td><td>1.04</td><td>1.27</td></tr> +<tr bgcolor="#eeeeee"><td>44</td><td>BXD32</td><td>R0898F1</td><td>e_B2</td><td><center>A</center></td><td>9.574</td><td>45.43</td><td>0.447</td><td>0.532</td><td>0.022</td><td>1.3</td><td>0.7</td></tr> +<tr bgcolor="#eeeeee"><td>44</td><td>BXD32</td><td>R0898F1</td><td>e_B2</td><td><center>B</center></td><td>28.57</td><td>42.93</td><td>0.23</td><td>0.752</td><td>0.019</td><td>1.42</td><td>0.69</td></tr> +<tr bgcolor="#eeeeee"><td>45</td><td>BXD32</td><td>R1214F1</td><td>w_B3</td><td><center>A</center></td><td>5.506</td><td>41.54</td><td>0.527</td><td>0.454</td><td>0.019</td><td>1.4</td><td>2.12</td></tr> +<!---<tr bgcolor="#eeeeee"><td>45</td><td>BXD32</td><td>R1214F1</td><td>w_B3</td><td><center>B</center></td><td>14.321</td><td>34.17</td><td>0.332</td><td>0.647</td><td>0.021</td><td>1</td><td>2.28</td></tr>---> +<tr bgcolor="#eeeeee"><td>46</td><td>BXD32</td><td>R1217F2</td><td>e_B4</td><td><center>A</center></td><td>1.861</td><td>68.71</td><td>0.581</td><td>0.404</td><td>0.015</td><td>1.62</td><td>0.89</td></tr> +<tr bgcolor="#eeeeee"><td>46</td><td>BXD32</td><td>R1217F2</td><td>e_B4</td><td><center>B</center></td><td>5.388</td><td>55.49</td><td>0.376</td><td>0.602</td><td>0.022</td><td>1.94</td><td>0.83</td></tr> +<tr bgcolor="#eeeeee"><td>47</td><td>BXD32</td><td>R1478F1</td><td>e_B3</td><td><center>A</center></td><td>5.452</td><td>42.1</td><td>0.52</td><td>0.46</td><td>0.019</td><td>1.36</td><td>1.68</td></tr> +<tr bgcolor="#eeeeee"><td>47</td><td>BXD32</td><td>R1478F1</td><td>e_B3</td><td><center>B</center></td><td>14.805</td><td>38.7</td><td>0.332</td><td>0.647</td><td>0.021</td><td>1.53</td><td>1.84</td></tr> +<tr bgcolor="#eeeeee"><td>48</td><td>BXD34</td><td>R0916F1</td><td>e_B2</td><td><center>A</center></td><td>5.377</td><td>55.95</td><td>0.446</td><td>0.534</td><td>0.021</td><td>1.12</td><td>0.75</td></tr> +<tr bgcolor="#eeeeee"><td>48</td><td>BXD34</td><td>R0916F1</td><td>e_B2</td><td><center>B</center></td><td>13.775</td><td>50.2</td><td>0.253</td><td>0.729</td><td>0.019</td><td>1.18</td><td>0.76</td></tr> +<tr bgcolor="#eeeeee"><td>49</td><td>BXD34</td><td>R0900F1</td><td>e_B3</td><td><center>A</center></td><td>7.206</td><td>45.6</td><td>0.484</td><td>0.495</td><td>0.021</td><td>1.11</td><td>1.15</td></tr> +<tr bgcolor="#eeeeee"><td>49</td><td>BXD34</td><td>R0900F1</td><td>e_B3</td><td><center>B</center></td><td>14.661</td><td>52.1</td><td>0.494</td><td>0.497</td><td>0.021</td><td>1.11</td><td>1.15</td></tr> +<tr bgcolor="#eeeeee"><td>50</td><td>BXD36</td><td>R2654F1</td><td>e_B4</td><td><center>A</center></td><td>2.646</td><td>53.84</td><td>0.559</td><td>0.424</td><td>0.017</td><td>1.89</td><td>1.27</td></tr> +<tr bgcolor="#eeeeee"><td>50</td><td>BXD36</td><td>R2654F1</td><td>e_B4</td><td><center>B</center></td><td>7.062</td><td>54.84</td><td>0.334</td><td>0.647</td><td>0.019</td><td>1.91</td><td>1.24</td></tr> +<tr bgcolor="#eeeeee"><td>51</td><td>BXD36</td><td>R1145F1</td><td>e_B3</td><td><center>A</center></td><td>5.229</td><td>41.48</td><td>0.515</td><td>0.466</td><td>0.019</td><td>0.97</td><td>1.12</td></tr> +<tr bgcolor="#eeeeee"><td>51</td><td>BXD36</td><td>R1145F1</td><td>e_B3</td><td><center>B</center></td><td>12.661</td><td>40.04</td><td>0.334</td><td>0.644</td><td>0.022</td><td>1.04</td><td>1.13</td></tr> +<tr bgcolor="#eeeeee"><td>52</td><td>BXD36</td><td>R0926F1</td><td>e_B2</td><td><center>A</center></td><td>5.841</td><td>55.5</td><td>0.438</td><td>0.541</td><td>0.021</td><td>1.26</td><td>0.74</td></tr> +<tr bgcolor="#eeeeee"><td>52</td><td>BXD36</td><td>R0926F1</td><td>e_B2</td><td><center>B</center></td><td>13.353</td><td>53.81</td><td>0.263</td><td>0.716</td><td>0.021</td><td>1.23</td><td>0.76</td></tr> +<tr bgcolor="#eeeeee"><td>53</td><td>BXD38</td><td>R0729F1</td><td>e_B3</td><td><center>A</center></td><td>5.472</td><td>83.41</td><td>0.469</td><td>0.512</td><td>0.019</td><td>0.92</td><td>1.09</td></tr> +<tr bgcolor="#eeeeee"><td>53</td><td>BXD38</td><td>R0729F1</td><td>e_B3</td><td><center>B</center></td><td>10.88</td><td>67.39</td><td>0.299</td><td>0.679</td><td>0.022</td><td>1.06</td><td>1.2</td></tr> +<tr bgcolor="#eeeeee"><td>54</td><td>BXD38</td><td>R1208F1</td><td>g_B3</td><td><center>A</center></td><td>3.532</td><td>43.38</td><td>0.544</td><td>0.438</td><td>0.018</td><td>1.15</td><td>1.27</td></tr> +<tr bgcolor="#eeeeee"><td>54</td><td>BXD38</td><td>R1208F1</td><td>g_B3</td><td><center>B</center></td><td>15.234</td><td>43.65</td><td>0.311</td><td>0.667</td><td>0.023</td><td>1.08</td><td>1.38</td></tr> +<tr bgcolor="#eeeeee"><td>55</td><td>BXD39</td><td>R1712F1</td><td>e_B3</td><td><center>A</center></td><td>7.514</td><td>44.54</td><td>0.49</td><td>0.489</td><td>0.021</td><td>1.69</td><td>1.42</td></tr> +<tr bgcolor="#eeeeee"><td>55</td><td>BXD39</td><td>R1712F1</td><td>e_B3</td><td><center>B</center></td><td>12.624</td><td>44.61</td><td>0.318</td><td>0.661</td><td>0.021</td><td>1.34</td><td>1.55</td></tr> +<!---<tr bgcolor="#eeeeee"><td>56</td><td>BXD39</td><td>R0602F1</td><td>w_B3</td><td><center>A</center></td><td>8.191</td><td>37.91</td><td>0.496</td><td>0.484</td><td>0.02</td><td>1.4</td><td>2.13</td></tr>---> +<tr bgcolor="#eeeeee"><td>56</td><td>BXD39</td><td>R0602F1</td><td>w_B3</td><td><center>B</center></td><td>20.231</td><td>37.07</td><td>0.301</td><td>0.68</td><td>0.02</td><td>1.07</td><td>2.33</td></tr> +<tr bgcolor="#eeeeee"><td>57</td><td>BXD40</td><td>R0741F1</td><td>e_B3</td><td><center>A</center></td><td>5.234</td><td>45.68</td><td>0.51</td><td>0.469</td><td>0.02</td><td>1.69</td><td>1.17</td></tr> +<tr bgcolor="#eeeeee"><td>57</td><td>BXD40</td><td>R0741F1</td><td>e_B3</td><td><center>B</center></td><td>12.242</td><td>46.89</td><td>0.323</td><td>0.656</td><td>0.021</td><td>1.12</td><td>1.23</td></tr> +<tr bgcolor="#eeeeee"><td>58</td><td>BXD40</td><td>R0894F1</td><td>e_B3</td><td><center>A</center></td><td>5.326</td><td>44.9</td><td>0.52</td><td>0.459</td><td>0.021</td><td>1.26</td><td>1.21</td></tr> +<tr bgcolor="#eeeeee"><td>58</td><td>BXD40</td><td>R0894F1</td><td>e_B3</td><td><center>B</center></td><td>10.339</td><td>41.24</td><td>0.352</td><td>0.625</td><td>0.024</td><td>0.81</td><td>1.4</td></tr> +<tr bgcolor="#eeeeee"><td>59</td><td>BXD42</td><td>R0742F1</td><td>e_B3</td><td><center>A</center></td><td>5.542</td><td>43.66</td><td>0.522</td><td>0.458</td><td>0.021</td><td>1.72</td><td>1.17</td></tr> +<tr bgcolor="#eeeeee"><td>59</td><td>BXD42</td><td>R0742F1</td><td>e_B3</td><td><center>B</center></td><td>15.095</td><td>41.37</td><td>0.319</td><td>0.66</td><td>0.022</td><td>1.27</td><td>1.24</td></tr> +<tr bgcolor="#eeeeee"><td>60</td><td>BXD43</td><td>R1199F1</td><td>e_B3</td><td><center>A</center></td><td>6.171</td><td>41.28</td><td>0.523</td><td>0.458</td><td>0.019</td><td>1.06</td><td>1.23</td></tr> +<tr bgcolor="#eeeeee"><td>60</td><td>BXD43</td><td>R1199F1</td><td>e_B3</td><td><center>B</center></td><td>16.534</td><td>40.32</td><td>0.291</td><td>0.685</td><td>0.024</td><td>0.99</td><td>1.54</td></tr> +<tr bgcolor="#eeeeee"><td>61</td><td>BXD43</td><td>R0980F1</td><td>e_B4</td><td><center>A</center></td><td>1.592</td><td>63.75</td><td>0.591</td><td>0.392</td><td>0.017</td><td>1.76</td><td>0.95</td></tr> +<tr bgcolor="#eeeeee"><td>61</td><td>BXD43</td><td>R0980F1</td><td>e_B4</td><td><center>B</center></td><td>5.815</td><td>48.89</td><td>0.378</td><td>0.601</td><td>0.021</td><td>2.06</td><td>0.97</td></tr> +<tr bgcolor="#eeeeee"><td>62</td><td>BXD44</td><td>R1072F1</td><td>e_B3</td><td><center>A</center></td><td>7.858</td><td>41.12</td><td>0.476</td><td>0.502</td><td>0.022</td><td>1.52</td><td>1.74</td></tr> +<tr bgcolor="#eeeeee"><td>62</td><td>BXD44</td><td>R1072F1</td><td>e_B3</td><td><center>B</center></td><td>23.065</td><td>41.32</td><td>0.264</td><td>0.717</td><td>0.019</td><td>1.25</td><td>1.84</td></tr> +<tr bgcolor="#eeeeee"><td>63</td><td>BXD45</td><td>R1398F1</td><td>o_B3</td><td><center>A</center></td><td>13.911</td><td>45.87</td><td>0.384</td><td>0.595</td><td>0.021</td><td>1.24</td><td>1.7</td></tr> +<tr bgcolor="#eeeeee"><td>63</td><td>BXD45</td><td>R1398F1</td><td>o_B3</td><td><center>B</center></td><td>40.07</td><td>47.47</td><td>0.178</td><td>0.805</td><td>0.017</td><td>1.21</td><td>1.68</td></tr> +<tr bgcolor="#eeeeee"><td>64</td><td>BXD45</td><td>R1658F2</td><td>e_B4</td><td><center>A</center></td><td>2.368</td><td>56.29</td><td>0.573</td><td>0.408</td><td>0.019</td><td>1.42</td><td>0.84</td></tr> +<tr bgcolor="#eeeeee"><td>64</td><td>BXD45</td><td>R1658F2</td><td>e_B4</td><td><center>B</center></td><td>7.006</td><td>49.52</td><td>0.372</td><td>0.608</td><td>0.02</td><td>1.45</td><td>0.8</td></tr> +<tr bgcolor="#eeeeee"><td>65</td><td>BXD48</td><td>R0946F1</td><td>e_B3</td><td><center>A</center></td><td>6.565</td><td>47.79</td><td>0.487</td><td>0.493</td><td>0.021</td><td>1.68</td><td>1.27</td></tr> +<tr bgcolor="#eeeeee"><td>65</td><td>BXD48</td><td>R0946F1</td><td>e_B3</td><td><center>B</center></td><td>17.499</td><td>41.87</td><td>0.292</td><td>0.687</td><td>0.021</td><td>1.54</td><td>1.35</td></tr> +<tr bgcolor="#eeeeee"><td>66</td><td>BXD51</td><td>R1430F1</td><td>e_B3</td><td><center>A</center></td><td>7.042</td><td>57.48</td><td>0.46</td><td>0.519</td><td>0.022</td><td>1.17</td><td>1.29</td></tr> +<tr bgcolor="#eeeeee"><td>66</td><td>BXD51</td><td>R1430F1</td><td>e_B3</td><td><center>B</center></td><td>19.373</td><td>48.26</td><td>0.259</td><td>0.72</td><td>0.021</td><td>2.07</td><td>1.48</td></tr> +<tr bgcolor="#eeeeee"><td>67</td><td>BXD51</td><td>R1001F1</td><td>e_B3</td><td><center>A</center></td><td>4.689</td><td>58.81</td><td>0.501</td><td>0.48</td><td>0.019</td><td>1.88</td><td>1.31</td></tr> +<tr bgcolor="#eeeeee"><td>67</td><td>BXD51</td><td>R1001F1</td><td>e_B3</td><td><center>B</center></td><td>16.032</td><td>55.59</td><td>0.266</td><td>0.715</td><td>0.019</td><td>1.31</td><td>1.64</td></tr> +<tr bgcolor="#eeeeee"><td>68</td><td>BXD60</td><td>R1075F1</td><td>g_B3</td><td><center>A</center></td><td>8.189</td><td>49.9</td><td>0.465</td><td>0.513</td><td>0.022</td><td>1.39</td><td>1.34</td></tr> +<tr bgcolor="#eeeeee"><td>68</td><td>BXD60</td><td>R1075F1</td><td>g_B3</td><td><center>B</center></td><td>19.219</td><td>45.14</td><td>0.277</td><td>0.705</td><td>0.018</td><td>1.77</td><td>1.41</td></tr> +<tr bgcolor="#eeeeee"><td>69</td><td>BXD62</td><td>R1027F1</td><td>e_B3</td><td><center>A</center></td><td>7.447</td><td>44.42</td><td>0.491</td><td>0.488</td><td>0.021</td><td>2.03</td><td>1.23</td></tr> +<tr bgcolor="#eeeeee"><td>69</td><td>BXD62</td><td>R1027F1</td><td>e_B3</td><td><center>B</center></td><td>19.391</td><td>41.09</td><td>0.285</td><td>0.696</td><td>0.019</td><td>1.05</td><td>1.44</td></tr> +<tr bgcolor="#eeeeee"><td>70</td><td>BXD69</td><td>R1438F1</td><td>e_B3</td><td><center>A</center></td><td>6.297</td><td>44.19</td><td>0.512</td><td>0.469</td><td>0.019</td><td>1.77</td><td>1.5</td></tr> +<tr bgcolor="#eeeeee"><td>70</td><td>BXD69</td><td>R1438F1</td><td>e_B3</td><td><center>B</center></td><td>12.335</td><td>46.58</td><td>0.311</td><td>0.667</td><td>0.021</td><td>1.25</td><td>1.62</td></tr> +<tr bgcolor="#eeeeee"><td>71</td><td>BXD69</td><td>R1193F1</td><td>o_B3</td><td><center>A</center></td><td>5.749</td><td>83.56</td><td>0.414</td><td>0.564</td><td>0.022</td><td>1.49</td><td>1.58</td></tr> +<tr bgcolor="#eeeeee"><td>71</td><td>BXD69</td><td>R1193F1</td><td>o_B3</td><td><center>B</center></td><td>20.513</td><td>44.28</td><td>0.261</td><td>0.718</td><td>0.021</td><td>1.14</td><td>1.58</td></tr> +<tr bgcolor="#eeeeee"><td>72</td><td>BXD73</td><td>R1275F1</td><td>e_B3</td><td><center>A</center></td><td>6.478</td><td>40.91</td><td>0.499</td><td>0.481</td><td>0.02</td><td>1.05</td><td>1.52</td></tr> +<tr bgcolor="#eeeeee"><td>72</td><td>BXD73</td><td>R1275F1</td><td>e_B3</td><td><center>B</center></td><td>16.931</td><td>41.6</td><td>0.299</td><td>0.681</td><td>0.02</td><td>1.62</td><td>1.53</td></tr> +<tr bgcolor="#eeeeee"><td>73</td><td>BXD73</td><td>R1442F1</td><td>g_B3</td><td><center>A</center></td><td>8.584</td><td>62.86</td><td>0.428</td><td>0.552</td><td>0.02</td><td>1.78</td><td>1.69</td></tr> +<tr bgcolor="#eeeeee"><td>73</td><td>BXD73</td><td>R1442F1</td><td>g_B3</td><td><center>B</center></td><td>17.378</td><td>55.71</td><td>0.26</td><td>0.72</td><td>0.02</td><td>1.17</td><td>1.83</td></tr> +<tr bgcolor="#eeeeee"><td>74</td><td>BXD77</td><td>R1426F1</td><td>g_B3</td><td><center>A</center></td><td>6.306</td><td>46.27</td><td>0.501</td><td>0.481</td><td>0.018</td><td>1.77</td><td>1.49</td></tr> +<tr bgcolor="#eeeeee"><td>74</td><td>BXD77</td><td>R1426F1</td><td>g_B3</td><td><center>B</center></td><td>13.365</td><td>48.96</td><td>0.309</td><td>0.67</td><td>0.022</td><td>1.26</td><td>1.63</td></tr> +<tr bgcolor="#eeeeee"><td>75</td><td>BXD87</td><td>R1713F1</td><td>e_B3</td><td><center>A</center></td><td>6.243</td><td>39.43</td><td>0.515</td><td>0.466</td><td>0.018</td><td>1.38</td><td>1.34</td></tr> +<tr bgcolor="#eeeeee"><td>75</td><td>BXD87</td><td>R1713F1</td><td>e_B3</td><td><center>B</center></td><td>14.997</td><td>42.78</td><td>0.305</td><td>0.673</td><td>0.022</td><td>1.71</td><td>1.58</td></tr> +<tr bgcolor="#eeeeee"><td>76</td><td>BXD90</td><td>R2628F1</td><td>e_B4</td><td><center>A</center></td><td>2.096</td><td>58.74</td><td>0.572</td><td>0.412</td><td>0.016</td><td>1.57</td><td>0.82</td></tr> +<tr bgcolor="#eeeeee"><td>76</td><td>BXD90</td><td>R2628F1</td><td>e_B4</td><td><center>B</center></td><td>8.913</td><td>49.12</td><td>0.332</td><td>0.646</td><td>0.023</td><td>1.88</td><td>0.85</td></tr> +<tr bgcolor="#eeeeee"><td>77</td><td>BXD90</td><td>R1452F</td><td>g_B3</td><td><center>A</center></td><td>7.478</td><td>52.26</td><td>0.449</td><td>0.531</td><td>0.02</td><td>1.17</td><td>1.74</td></tr> +<tr bgcolor="#eeeeee"><td>77</td><td>BXD90</td><td>R1452F</td><td>g_B3</td><td><center>B</center></td><td>15.469</td><td>40.59</td><td>0.312</td><td>0.668</td><td>0.02</td><td>1.7</td><td>1.74</td></tr> +<tr bgcolor="#eeeeee"><td>78</td><td>BXD92</td><td>R1299F1</td><td>e_B3</td><td><center>A</center></td><td>8.264</td><td>45.38</td><td>0.478</td><td>0.503</td><td>0.019</td><td>1.4</td><td>1.37</td></tr> +<tr bgcolor="#eeeeee"><td>78</td><td>BXD92</td><td>R1299F1</td><td>e_B3</td><td><center>B</center></td><td>18.369</td><td>43.4</td><td>0.29</td><td>0.689</td><td>0.021</td><td>1.91</td><td>1.6</td></tr> </table> +</td> +</tr> +</table> +</Blockquote> + + +<P class="subtitle"> About data access:</P> +<Blockquote> + +<P>Normalized data are available for this INIA data set at</P> +<Blockquote> +<OR> + +<LI>Jan 2006, PDNN normalization (17 Mb file with strain means): <A HREF="ftp://atlas.utmem.edu/Public/Mouse_bxd/INIA_M_0106_PDNN.txt">ftp://atlas.utmem.edu/Public/Mouse_bxd/INIA_M_0106_PDNN.txt </A> + +<LI>Jan 2006, RMA normalization (17 Mb file with strain means): <A HREF="ftp://atlas.utmem.edu/Public/Mouse_bxd/INIA_M_0106_RMA.txt">ftp://atlas.utmem.edu/Public/Mouse_bxd/INIA_M_0106_RMA.txt </A> + +<LI>June 2006, QTL results from RMA normalized data (5.7 Mb, no strain means): <A HREF="ftp://atlas.utmem.edu/Public/Mouse_bxd/INIA_M_0606_RMA.txt">ftp://atlas.utmem.edu/Public/Mouse_bxd/INIA_M_0606_RMA.txt </A> + +<LI>All data in ZIP format: <A HREF="ftp://atlas.utmem.edu/Public/Mouse_bxd/INIA_mRNA_data_sets.zip">ftp://atlas.utmem.edu/Public/Mouse_bxd/INIA_mRNA_data_sets.zip </A> +</OR> + +</Blockquote> +</Blockquote> + + + + +<P class="subtitle"> About the array platform:</P> +<Blockquote> +<P><B>Affymetrix Mouse Genome 430A and B array pairs: </B>The <A HREF="http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20" target="_blank" class="normal">430A and B</A> array pairs consist of 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430 2.0 series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0</P> +</Blockquote> + + +<P class="subtitle"> About data processing:</P> + +<Blockquote><B>Probe (cell) level data from the CEL file: </B>These CEL values produced by <a target="_blank" class="fs14" href="http://www.affymetrix.com/support/technical/product_updates/gcos_download.affx">GCOS</a> are 75% quantiles from a set of 91 pixel values per cell. +<UL> + +<LI>Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell. + +<LI>Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform. + +<LI>Step 3: We computed the Z scores for each cell value. + +<LI>Step 4: We multiplied all Z scores by 2. + +<LI>Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference. + +<LI>Step 6: We eliminated much of the systematic technical variance introduced by the two batches (n = 34 and n = 71 array pairs) at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same. + +<LI>Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5. + +<LI>Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5. + +<LI>Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables. + +</UL> + + +<B>Probe set data: </B>The expression data were processed by Yanhua Qu (UTHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (<a target="_blank" href="http://www.bioconductor.org" class="fs14">RMA</a>) method (Irrizary et al. 2003). Values were log2 transformed. Probe set values listed in WebQTL are the averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels. +<UL> +<LI>Setp 1: Get CAB file for all arrays (121 arrays) +<LI>Setp 2: Unpack CAB file using GCOS 1.4 DAT, CEL, RPT, CHP +<LI>Setp 3: Put RPT data into spreadsheet +<LI>Setp 4: Remaining N CEL data files were transformed to old CEL format using Transfer Tool (121 arrays) +<LI>Setp 5: Old CEL format files transformed using RMA and PDNN (121 arrays). 430A set and 430B set arrays are processed separately using RMA and PDNN, Normalize 430A and 430B separately to Z Scores (2Z+8). +<LI>Setp 6: Examine all scatter plots of the probe sets using DataDesk and categorized them by similarity. We are looking for batch and sub-batch structure. There are still quite obvious differences. For the INIA data we defined 5 groups that did NOT align exactly with the batches. The results are indicated in the table under the heading "Final Grouping." These are letters followed by the batch. For example "e_2" is an "e" type data set from batch 2. The prefix "s" means that an array was considered the "standard" for a particular group. For example sgA_2 is the "standard" for the gA group and was a member of batch 2. We defined groups "e" (originally "e" stood for 'excellent'), "g" (originally 'g' stood for good), "o" (OK), "w" (wide), and "gA" (good subdivision A). +<LI>Setp 7: Delete obviously bad arrays (n of 3 were deleted, leaving 118 arrays). Array BXD8(S167) is high scale factor (A:16.797,B:35.646); BXD18(R1220) and BXD33(R2627) are high 3'/5' B_Act_Sig(64.20), GAPD_Sig(84.20) and B_Act_Sig(49.92), GAPD_Sig(84.17). +<LI>Setp 8: Group rescale four minor groups to the same level of the largest group (please note that a group may have arrays from multiple physical batches). This group correction is done on a probe_set-by-probe_set level. The result of this rescaling is a group corrected data set. +<LI>Setp 9: Look at the group rescaled arrays and delete any arrays that do not look "good" where good is usually a correlation of >0.96 with respect to other arrays. For the INIA data set of 118 arrays we deleted 40 arrays using very strict "goodness" criteria. +<LI>Setp 10: Reprocess the remaining 78 good old-format CEL files and process as in Step 5. , 430A set and 430B set separately using RMA and PDNN, Normalize 430A and 430B separately to Z Scores (2Z+8). +<LI>Setp 11: Bring the two arrays (430A and 430B) into alignment. To do this we regressed Z scores of the common set of 100 probe sets to obtain a linear regression corrections to rescale the 430B arrays to the 430A array values. Make data sets for RMA_430AB and PDNN_430AB. Normalize 430AB to Z Scores. +<LI>Setp 12:Rank order of Probe Sets: Run all of the arrays through a second quantile normalization. This involves computing the average of all probe sets across all arrays. These averages are then rank ordered. We also rank order each of the individual array data sets. Probe sets for each individual array are then assigned a new expression value based on 1. Its rank within the particular array and 2. the value of that particular rank taken from the AVERAGE data. This forces every array to have exactly the same distribution as the average data. The result of this process is colinear expression of all arrays. +<LI>Setp 13: We normalize the means of each of these groups to a common value set to the largest group (group e now with 37 members). If the mean for probe set 100001 is 8 in group e whereas group g a mean 8.5, then we just have a correction factor of 8/8.5 for probe set 100001 in the group g. The intent of this step is to correct for group effect on a probe set by probe set level. +<LI>Setp 14: Verify that all arrays have correlations >0.98 using RMA transform. Two arrays discovered that escaped deletion. Delete these arrays (BXD32-R1214, BXD39-R0602) +<LI>Setp 15: Finally, we compute the arithmetic mean of the values for the set of 76 final arrays for each strain. +</UL> +<P>This data set include further normalization to produce final estimates of expression that can be compared directly to the other transforms (average of 8 units and stabilized standard deviation of 2 units within each array). Please see Bolstad and colleagues (<A href="http://www.stat.berkeley.edu/users/bolstad/normalize/normalize.html" class="fs14">2003</A>) for a helpful comparison of RMA and two other common methods of processing Affymetrix array data sets. +</Blockquote> + + +<P class="subtitle"> About the chromosome and megabase position values:</P> + +<Blockquote>The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 Assembly (see <a href="http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse" class="fs14">http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse</a>). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.</Blockquote> + + +<P class="subtitle"> Data source acknowledgment:</P> +<Blockquote> +Support for acquisition of microarray data were generously provided by the NIAAA and its INIA grant program to RWW, Thomas Sutter, and Daniel Goldowitz (U01AA013515, U01AA013499-03S1, U01AA013488, U01AA013503-03S1). Support for the continued development of the GeneNetwork and WebQTL was provided by a NIMH Human Brain Project grant (P20MH062009). All arrays were processed at the University of Memphis by Thomas Sutter and colleagues with support of the INIA Bioanalytical Core. +</Blockquote> + +<P class="subtitle"> Information about this text file:</P> +<Blockquote><P>This text file originally generated by RWW Nov 29, 2006 using as a template the previous Jan06 RMA INFO file. +</P></Blockquote> + +<P></P> + +</TD> +</TR></TABLE> +</TD> +</TR> +<TR> +<TD align=center bgColor=#ddddff class="solidBorder"> + + + +<!--Start of footer--> +<TABLE width="90%"> +<script language='JavaScript' src='/javascript/footer.js'></script> +</TABLE> +<!--End of footer--> + + + +</TD> +</TR> +</TABLE> +<!-- /Footer --> +<!-- menu script itself. you should not modify this file --> +<script language="JavaScript" src="/javascript/menu_new.js"></script> +<!-- items structure. menu hierarchy and links are stored there --> +<script language="JavaScript" src="/javascript/menu_items.js"></script> +<!-- files with geometry and styles structures --> + +<script language="JavaScript" src="/javascript/menu_tpl.js"></script> +<script language="JavaScript"> +<!--// +// Note where menu initialization block is located in HTML document. +// Don't try to position menu locating menu initialization block in +// some table cell or other HTML element. 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