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diff --git a/general/datasets/G2nei_ilm_retina_bxd_ri0410/experiment-design.rtf b/general/datasets/G2nei_ilm_retina_bxd_ri0410/experiment-design.rtf new file mode 100644 index 0000000..4fff707 --- /dev/null +++ b/general/datasets/G2nei_ilm_retina_bxd_ri0410/experiment-design.rtf @@ -0,0 +1,12 @@ +<p>Expression profiling by array</p>
+
+<p>We used pooled RNA samples of retinas, usually two independent pools--two male, two female pool--for most lines of mice.</p>
+
+<p>All normalization was performed by William E. Orr in the HEI Vision Core Facility</p>
+
+<ol>
+ <li>Computed the log base 2 of each raw signal value</li>
+ <li>Calculated the mean and standard Deviation of each Mouse WG-6 v2.0 array</li>
+ <li>Normalized each array using the formula, 2 (z-score of log2 [intensity]) The result is to produce arrays that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.</li>
+ <li>computed the mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.</li>
+</ol>
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