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Diffstat (limited to 'general/datasets/BRF2_M_0304_P/processing.rtf')
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diff --git a/general/datasets/BRF2_M_0304_P/processing.rtf b/general/datasets/BRF2_M_0304_P/processing.rtf new file mode 100644 index 0000000..002c868 --- /dev/null +++ b/general/datasets/BRF2_M_0304_P/processing.rtf @@ -0,0 +1,16 @@ +<p>The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within <a class="normal" href="http://biostat.jhsph.edu/~kbroman/qtl" target="_blank">R/qtl</a> (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.</p>
+
+<p><strong>Probe (cell) level data from the CEL file: </strong>These CEL values produced by <a class="normal" href="http://www.affymetrix.com/support/technical/product_updates/gcos_download.affx" target="_blank">GCOS</a> are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:</p>
+
+<ul>
+ <li>Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.</li>
+ <li>Step 2: We took the log2 of each probe signal.</li>
+ <li>Step 3: We computed the Z score for each signal within array.</li>
+ <li>Step 4: We multiplied all Z scores by 2.</li>
+ <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>
+ <li>Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.</li>
+</ul>
+
+<p><strong>Probe set data from the TXT file: </strong>These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.</p>
+
+<p>The chromosomal locations of M430A and M430B probe sets were determined by <a class="normal" href="http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse" target="_blank">BLAT</a> analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the <strong>Verify</strong> link in the Trait Data and Editing Form (right side of the <strong>Location</strong> line).</p>
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