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diff --git a/general/datasets/Dodcmmrpretmogene2_0515/experiment-design.rtf b/general/datasets/Dodcmmrpretmogene2_0515/experiment-design.rtf new file mode 100644 index 0000000..6256015 --- /dev/null +++ b/general/datasets/Dodcmmrpretmogene2_0515/experiment-design.rtf @@ -0,0 +1,3 @@ +<p>ll of the procedures used involving mice were approved by IACUC at the Emory University and adhered to the ARVO Statement for the Use of Animals in Research. The Department of Defense (DoD) Congressionally Directed Medical Research Programs (CDMRP) Normal Retina Database uses the Affymetrix MouseGene 2.0 ST Array (May 15, 2015). Robust multiarray average (RMA) analysis and scaling were conducted by Arthur Centeno. This data set consists of 52 BXD strains, C57BL/6J, DBA/2J, and an F1 cross between C57BL/6J and DBA/2J. A total of 55 strains were quantified. There is a total of 222 microarrays. All data from each microarray used in this data set is publicly available on <a href="http://www.genenetwork.org/" style="color: rgb(79, 49, 87);">GeneNetwork</a>.</p>
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+<p>These are RMA expression data that have been normalized using what we call a 2<em>z</em>+8 scale, but without corrections for batch effects. The data for each strain were computed as the mean of four samples per strain. The expression values on the log<sub>2</sub> scale ranged from 3.81 to 14.25 (10.26 units), a nominal range of approximately 1,000-fold. After taking the log<sub>2</sub> of the original non-logged expression estimates, we converted the data within an array to a z-score. We then multiplied the z-score by 2. Finally, we added 8 units to ensure that no values were negative. The result was a scale with the mean expression of the probes on the array of 8 units and a standard deviation of 2 units. A twofold difference in expression is equivalent to roughly 1 unit on this scale. The lowest level of expression was 3.81 (<em>Olfr1186</em>) from the DoD CDMRP (the Normal Retina Database uses the Affymetrix MouseGene 2.0 ST Array, May 15, 2015). The highest level of expression was rhodopsin for <em>17462036</em> (Rho). The highest single value was 14.25.</p>
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