From d029d5d7f8ead1f1de8d318045004a4a6f68f5fb Mon Sep 17 00:00:00 2001
From: Bonface
Date: Fri, 9 Feb 2024 09:41:28 -0600
Subject: Update dataset RTF Files.

---
 general/datasets/LVF2_M_0704_R/processing.rtf | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 general/datasets/LVF2_M_0704_R/processing.rtf

(limited to 'general/datasets/LVF2_M_0704_R/processing.rtf')

diff --git a/general/datasets/LVF2_M_0704_R/processing.rtf b/general/datasets/LVF2_M_0704_R/processing.rtf
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+<blockquote><strong>Probe (cell) level data from the CEL file: </strong>These CEL values produced by <a class="fs14" href="http://www.affymetrix.com/support/technical/product_updates/gcos_download.affx" target="_blank">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 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 log base 2 of each cell.</li>
+	<li>Step 3: We computed the Z scores for each cell.</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 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections 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 very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.</li>
+	<li>Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.</li>
+</ul>
+<strong>Probe set data from the .CHP file: </strong>The expression data were generated using <a href="http://www.affymetrix.com/products/software/specific/mas.affx" target="_blank">MAS5</a>. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.</blockquote>
+
+<blockquote>The 60 mice were each genotyped at 194 MIT microsatellite markers an average of approximately 10 cM (and always &lt; 30 cM) apart across the entire genome (Y chromsome, excepted). The genotyping error-check routine implemented within R/qtl (Broman et al. 2003) showed no likely errors at p &lt;0.01 probability.</blockquote>
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