Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

author: zsloan 2015-03-27 20:28:51 +0000
committer: zsloan 2015-03-27 20:28:51 +0000
commit: d0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree: 3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/dbdoc/UMUTAffyExon_0209_RMA.html
parent: a840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
download: genenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
1 files changed, 0 insertions, 254 deletions
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-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<HTML><HEAD><TITLE>UMUTAffy Hippocampus Exon (Feb09) RMA</TITLE>
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-<P class="title">UMUTAffy Hippocampus Exon (Feb09) 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=206">GN206</A></P>
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-<P>Data generated by RW Williams, Lu Lu, Manjunatha Jagalur, and David Kulp. All arrays run at the VA Medical Center, Memphis, by Yan Jiao.
-
-<P>Data entered by Arthur Centeno and Manju Jagalur, Feb 27, 2009. This data set modified data for two BXD strains. Data were added for BXD79 that had been incorrectly included as a striatum sample (this data set was therefore deleted from the Exon 1.0ST striatum data set). We also changed data for BXD39. As expected, this addition and correction improved QTL mapping values. For example, for Kcnj9 probe set 4519178 the LRS values increased from 103.3 in the Aug08 data to 115.7 for these Feb09 data. Rob is concerned about the high error term of BXD39.</p>
-
-<A>Quality improvement of BXD data	</A>
-<BR>
-The following steps were applied to refine the data by M. Jagalur in RWW lab:
-<OL>
-<LI>Strain correction: In this step the strong probe level cis-QTLs were identified and using an expectation maximization (EM)-like method, the genotypes of each marker was re-assigned. This set of reassigned markers was compared to existing list genotypes of BXD strains and the maximal match was identified as the correct strain.
-<BR>
-&nbsp;&nbsp;	Results: Three chips were initially found to be strain-mislabeled.<BR>
-
-<LI>Sex correction: In this step probes that are highly correlated to sex were identified and using an EM-like method we detected and corrected the sex of single array data sets.<BR>
-&nbsp;&nbsp;	Results: Two chips were found to be sex-mislabeled <BR>
-
-<LI> Data exclusion criteria: In this step individual arrays were evaluated. Arrays were systematically excluded from the data set (drop one out)  and the number of cis-QTLs was recomputed. If excluding an array resulted in s significantly higher number of cis-QTLs then that array was considered to be of poor quality and was excluded from the final data set This step was repeated across all arrays in multiple cycles until there was no improvement in number of cis-QTLs <BR>
-Results: None of the arrays were dropped. <BR>
-
-<LI>Tissue correction: In this step probes that are highly correlated to tissue type were identified and EM-like method was used to identify correct tissue.<BR>
-&nbsp;&nbsp;Results: Three arrays were found to have been reverse labeled between hippocampus and striatum data sets. Samples were relabeled and reassigned based upon this analysis. <BR>
-
-<LI>Noise Removal: A noise component was calculated using the expression of "unhybridized" probes  (those with the lowest signal) and was removed from the data.
-<BR>
-&nbsp;&nbsp; Result: A spurious transband was detected on distal chromosome 12 and removed.
-</OL>
-
-
-<P>After this procedure we analyzed probe sets (n = 64) with the lowest expression (mean between 4.0 to 4.2). These probe sets had no cis eQTLs, confirming the absence of any significant biological variance in their expression. These background probe sets also did not have any notable transband expression pattern using the QTL heatmap function in GeneNetwork. This confirms that residual noise in this data set does not by chance covary well with any genetic markers. The covariation among this set of probe sets is poor. However, a small subset of probe sets do covary and generate a principal component that in total accounts for 25% the variance among this "noise" set. The first PC does not map well to any region.  (RWW June 2010).
-
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-<table width="600" border="0" cellpadding="5" cellspacing="1" align="left">
-<tr bgcolor="royalblue"><td><font color=#FFFFFF>Index</font></td><td><font color=#FFFFFF>Original CEL</font></td><td><font color=#FFFFFF>Tube ID</font></td><td><font color=#FFFFFF>Strain</font></td><td><font color=#FFFFFF>Age</font></td><td><font color=#FFFFFF>Sex</font></td><td><font color=#FFFFFF>Source</font></td></tr>
-<tr bgcolor="#eeeeee"><td>1</td><td>JR3551H.CEL</td><td>jr3551h</td><td>C57BL/6J</td><td>60</td><td>F</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>2</td><td>JR3552H.CEL</td><td>jr3552hre</td><td>C57BL/6J</td><td>60</td><td>F</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>3</td><td>R0572H.CEL</td><td>r0572h</td><td>C57BL/6J</td><td>69</td><td>F</td><td></td></tr>
-<tr bgcolor="#eeeeee"><td>4</td><td>R2137H.CEL</td><td>r2137h</td><td>C57BL/6J</td><td>55</td><td>F</td><td>JAX</td></tr>
-<tr bgcolor="#eeeeee"><td>5</td><td>R3552H.CEL</td><td>r3552h</td><td>C57BL/6J</td><td>60</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>6</td><td>JR3549H.CEL</td><td>jr3549h</td><td>C57BL/6J</td><td>60</td><td>M</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>7</td><td>JR3550H.CEL</td><td>jr3550hre</td><td>C57BL/6J</td><td>60</td><td>M</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>8</td><td>R0574H.CEL</td><td>r0574h</td><td>C57BL/6J</td><td>69</td><td>M</td><td></td></tr>
-<tr bgcolor="#eeeeee"><td>9</td><td>R2136H.CEL</td><td>r2136h</td><td>C57BL/6J</td><td>55</td><td>M</td><td>JAX</td></tr>
-<tr bgcolor="#eeeeee"><td>10</td><td>R3549H.CEL</td><td>r3549h</td><td>C57BL/6J</td><td>60</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>11</td><td>JR3557H.CEL</td><td>jr3557h</td><td>DBA/2J</td><td>60</td><td>F</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>12</td><td>JR3558H.CEL</td><td>jr3558hre</td><td>DBA/2J</td><td>60</td><td>F</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>13</td><td>R3558H.CEL</td><td>r3558h</td><td>DBA/2J</td><td>60</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>14</td><td>JR3555H.CEL</td><td>jr3555h</td><td>DBA/2J</td><td>60</td><td>M</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>15</td><td>JR3556H.CEL</td><td>jr3556h</td><td>DBA/2J</td><td>60</td><td>M</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>16</td><td>R3555H.CEL</td><td>r3555h</td><td>DBA/2J</td><td>60</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>17</td><td>R3497H.CEL</td><td>r3497h</td><td>B6D2F1</td><td>58</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>18</td><td>R3500H.CEL</td><td>r3500h</td><td>B6D2F1</td><td>58</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>19</td><td>R1374H.CEL</td><td>r1374h</td><td>D2B6F1</td><td>58</td><td>F</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>20</td><td>R1382H.CEL</td><td>r1382h</td><td>D2B6F1</td><td>59</td><td>M</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>21</td><td>R3532H.CEL</td><td>r3532h</td><td>129S1/SvImJ</td><td>60</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>22</td><td>R3512H.CEL</td><td>r3512h</td><td>129S1/SvImJ</td><td>59</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>23</td><td>R3520H.CEL</td><td>r3520h</td><td>A/J</td><td>59</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>24</td><td>R3523H.CEL</td><td>r3523h</td><td>A/J</td><td>59</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>25</td><td>R3514H.CEL</td><td>r3514h</td><td>AKR/J</td><td>59</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>26</td><td>R3515H.CEL</td><td>r3515h</td><td>AKR/J</td><td>59</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>27</td><td>R3508H.CEL</td><td>r3508h</td><td>BALB/cByJ</td><td>59</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>28</td><td>R3505H.CEL</td><td>r3505h</td><td>BALB/cByJ</td><td>59</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>29</td><td>R3524H.CEL</td><td>r3524h</td><td>BTBR T+ tf/J</td><td>60</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>30</td><td>R3509H.CEL</td><td>r3509h</td><td>BTBR T+ tf/J</td><td>60</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>31</td><td>R1542H.CEL</td><td>r1542h</td><td>BXD1</td><td>59</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>32</td><td>R1520H.CEL</td><td>r1520h</td><td>BXD2</td><td>56</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>33</td><td>R1694H.CEL</td><td>r1694h</td><td>BXD5</td><td>58</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>34</td><td>R3454H.CEL</td><td>r3454h</td><td>BXD6</td><td>58</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>35</td><td>R3457H.CEL</td><td>r3457h</td><td>BXD8</td><td>61</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>36</td><td>R3455H.CEL</td><td>r3455h</td><td>BXD9</td><td>60</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>37</td><td>R3462H.CEL</td><td>r3462h</td><td>BXD11</td><td>59</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>38</td><td>R3464H.CEL</td><td>r3464h</td><td>BXD12</td><td>59</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>39</td><td>R2315H.CEL</td><td>r2315h</td><td>BXD13</td><td>84</td><td>M</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>40</td><td>R3480H.CEL</td><td>r3480h</td><td>BXD14</td><td>60</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>41</td><td>R3478H.CEL</td><td>r3478h</td><td>BXD15</td><td>60</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>42</td><td>R3482H.CEL</td><td>r3482h</td><td>BXD16</td><td>59</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>43</td><td>R3488H.CEL</td><td>r3488h</td><td>BXD18</td><td>59</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>44</td><td>R3471H.CEL</td><td>r3471h</td><td>BXD19</td><td>60</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>45</td><td>R2506H.CEL</td><td>r2506h</td><td>BXD20</td><td>60</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>46</td><td>R3490H.CEL</td><td>r3490h</td><td>BXD21</td><td>60</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>47</td><td>R3492H.CEL</td><td>r3492h</td><td>BXD22</td><td>60</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>48</td><td>R3486H.CEL</td><td>r3486h</td><td>BXD23</td><td>60</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>49</td><td>R1547H.CEL</td><td>r1547h</td><td>BXD24</td><td>59</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>50</td><td>R2892H.CEL</td><td>r2892h</td><td>BXD25</td><td>67</td><td>F</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>51</td><td>R3485H.CEL</td><td>r3485h</td><td>BXD27</td><td>60</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>52</td><td>R3477H.CEL</td><td>r3477h</td><td>BXD28</td><td>60</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>53</td><td>R3475H.CEL</td><td>r3475h</td><td>BXD29</td><td>60</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>54</td><td>R3456H.CEL</td><td>r3456h</td><td>BXD31</td><td>60</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>55</td><td>R3570H.CEL</td><td>r3570h</td><td>BXD32</td><td>66</td><td>F</td><td></td></tr>
-<tr bgcolor="#eeeeee"><td>56</td><td>R3571H.CEL</td><td>r3571h</td><td>BXD32</td><td>58</td><td>M</td><td></td></tr>
-<tr bgcolor="#eeeeee"><td>57</td><td>R3467H.CEL</td><td>r3467h</td><td>BXD33</td><td>59</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>58</td><td>R3466H.CEL</td><td>r3466h</td><td>BXD34</td><td>60</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>59</td><td>R3463H.CEL</td><td>r3463h</td><td>BXD36</td><td>61</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>60</td><td>R3458H.CEL</td><td>r3458h</td><td>BXD38</td><td>55</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>61</td><td>JR4433H.CEL</td><td>jr4433sa</td><td>BXD39</td><td>63</td><td>F</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>62</td><td>R1535H.CEL</td><td>r1535h</td><td>BXD39</td><td>60</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>63</td><td>R3459H.CEL</td><td>r3459h</td><td>BXD40</td><td>60</td><td>M</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>64</td><td>R1541H.CEL</td><td>r1541h</td><td>BXD42</td><td>58</td><td>F</td><td>Glenn</td></tr>
-<tr bgcolor="#eeeeee"><td>65</td><td>R1279H.CEL</td><td>r1279h</td><td>BXD43</td><td>57</td><td>M</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>66</td><td>R1472H.CEL</td><td>r1472h</td><td>BXD45</td><td>65</td><td>M</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>67</td><td>R1586H.CEL</td><td>r1586h</td><td>BXD48</td><td>59</td><td>F</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>68</td><td>R2936H.CEL</td><td>r2936h</td><td>BXD50</td><td>61</td><td>F</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>69</td><td>R1313H.CEL</td><td>r1313h</td><td>BXD51</td><td>62</td><td>M</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>70</td><td>JR2680H.CEL</td><td>jr2680h</td><td>BXD55</td><td>65</td><td>M</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>71</td><td>R1340H.CEL</td><td>r1340h</td><td>BXD60</td><td>64</td><td>F</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>72</td><td>R1856H.CEL</td><td>r1856h</td><td>BXD61</td><td>94</td><td>M</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>73</td><td>R1317H.CEL</td><td>r1317h</td><td>BXD62</td><td>59</td><td>F</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>74</td><td>R1945H.CEL</td><td>r1945h</td><td>BXD63</td><td>107</td><td>F</td><td>UTM RW</td></tr>
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-<tr bgcolor="#eeeeee"><td>76</td><td>R3567H.CEL</td><td>r3567h</td><td>BXD65</td><td>60</td><td>F</td><td>UTRW</td></tr>
-<tr bgcolor="#eeeeee"><td>77</td><td>R1949H.CEL</td><td>r1949h</td><td>BXD66</td><td>96</td><td>M</td><td>UTM RW</td></tr>
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-<tr bgcolor="#eeeeee"><td>79</td><td>R2902H.CEL</td><td>r2902h</td><td>BXD68</td><td>57</td><td>M</td><td>UTM RW</td></tr>
-<tr bgcolor="#eeeeee"><td>80</td><td>R1466H.CEL</td><td>r1466h</td><td>BXD69</td><td>59</td><td>F</td><td>UTM RW</td></tr>
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-<tr bgcolor="#eeeeee"><td>83</td><td>JR2316H.CEL</td><td>jr2316hre</td><td>BXD74</td><td>193</td><td>M</td><td>UTM RW</td></tr>
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-<tr bgcolor="#eeeeee"><td>91</td><td>R3566H.CEL</td><td>r3566h</td><td>BXD85</td><td>65</td><td>M</td><td>UTRW</td></tr>
-<tr bgcolor="#eeeeee"><td>92</td><td>R1556H.CEL</td><td>r1556h</td><td>BXD86</td><td>57</td><td>F</td><td>UTM RW</td></tr>
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-</table>
-
-</td>
-</tr>
-</table>
-</Blockquote>
-</p>
-<P>We thank Affymetrix Inc. for their generous support of this project and array data set.
-<Blockquote>
-<P>Table updated by Rob with questions for Arthur, Aug 13, 2009.
-
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author	zsloan	2015-03-27 20:28:51 +0000
committer	zsloan	2015-03-27 20:28:51 +0000
commit	d0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree	3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/dbdoc/UMUTAffyExon_0209_RMA.html
parent	a840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
download	genenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz