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diff --git a/general/datasets/Dodcmmrpretmogene2_0515/summary.rtf b/general/datasets/Dodcmmrpretmogene2_0515/summary.rtf new file mode 100644 index 0000000..c79428d --- /dev/null +++ b/general/datasets/Dodcmmrpretmogene2_0515/summary.rtf @@ -0,0 +1,3 @@ +<p>The DoD (Department of Defense) CDMRP (Congressionally Directed Medical Research Programs) Normal Retina Database uses the Affymetrix MouseGene 2.0 ST Array (May 15 2015) The RMA analysis and scaling was conducted by Arthur Centeno. This data set consists of 55 BXD strains, C57BL/6J, DBA/2J, a F1 cross between C57BL/6J and DBA/2J. A total of 58 strains were quantified. There is a total of 222 microarrays.</p>
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+<p>This is RMA expression data that has been normalized using what we call a 2z+8 scale, but without special correction for batch effects. The data for each strain was computed as the mean of four samples per strain. Expression values on a log2 scale range from 3.81 to 14.25 (10.26 units), a nominal range of approximately 1,000-fold. After taking the log2 of the original non-logged expression estimates, we convert data within an array to a z score. We then multiply the z score by 2. Finally, we add 8 units to ensure that no values are negative. The result is a scale with a mean expression of the probes on the array of 8 units and a standard deviation of 2 units. A two-fold difference in expression is equivalent roughly to 1 unit on this scale. The lowest level of expression is 3.81 (Olfr1186) from DoD CDMRP (Normal Retina Database uses the Affymetrix MouseGene 2.0 ST Array (May 15 2015) The highest level of expression is Rhodopsin for 17462036 (Rho). Highest single value is about 14.25.</p>
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