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/ONCRetExMoGene2_0413/summary.rtf | 1 + 1 file changed, 1 insertion(+) create mode 100644 general/datasets/ONCRetExMoGene2_0413/summary.rtf (limited to 'general/datasets/ONCRetExMoGene2_0413/summary.rtf') diff --git a/general/datasets/ONCRetExMoGene2_0413/summary.rtf b/general/datasets/ONCRetExMoGene2_0413/summary.rtf new file mode 100644 index 0000000..96a87e5 --- /dev/null +++ b/general/datasets/ONCRetExMoGene2_0413/summary.rtf @@ -0,0 +1 @@ +

The DoD dataset was constructed using the Affymetrics GeneChip® Mouse Gene 2.0 ST microarrays. This relatively recent microarray was specifically designed to represent the whole-transcriptome. It includes probes to measure mRNA, long intergenic non-coding RNAs and microRNAs. Researchers have identified many transcripts in the mouse genome that do not have protein coding potential. Most of these non-coding RNAs have little functional annotation. There is considerable evidence that these non-coding RNAs play important roles in development of the retina and the progression of disease. The coverage in the new ST 2.0 array includes over 28,000 coding transcripts and over 7,000 non-coding transcripts. There are also probes on the array covering 590 microRNAs. 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 strains were computed as the mean of four samples per strain. Expression values on a log2 scale range from 3.77 to 14.62, a nominal range of approximately 3600-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 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.

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