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Diffstat (limited to 'general/datasets/GSE15222_F_A_RI_0409/platform.rtf')
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diff --git a/general/datasets/GSE15222_F_A_RI_0409/platform.rtf b/general/datasets/GSE15222_F_A_RI_0409/platform.rtf new file mode 100644 index 0000000..5bcda8b --- /dev/null +++ b/general/datasets/GSE15222_F_A_RI_0409/platform.rtf @@ -0,0 +1,5 @@ +<p>Illumina Human 50 mer probes. Total of 24357 probes according to Myers et al. A total of 24354 probes included in this GeneNetwork file.</p>
+
+<p>From the Methods section of the paper:</p>
+
+<p>Genotyping and Expression Proï¬ling DNA was hybridized to the Affymetrix GeneChip Human Mapping 500K Array Set (502,627 SNPs) as previously described.11,12 Genotypes were extracted with the use of both SNiPer-HD13 and BRLMM (Affymetrix, Santa Clara, CA) algorithms. Genotypes that exhibited less than 98% concordance between calls were excluded. SNPs with call rates less than 90% were excluded from the analysis. HardyWeinberg equilibrium (HWE) was assessed with exact tests and the PLINK analysis toolset.14 SNPs with HWE exact-test p values less than 0.05, as well as SNPs with minor-allele frequencies less than 1%, were excluded. Allele calls had a mean of 97% and a range of 90%–99%. cRNA was hybridized to Illumina Human Refseq-8 Expression BeadChip (24,357 transcripts) via standard protocols. Expression proï¬les were extracted and rank invariant normalized15–17 with the use of the BeadStudio software available from Illumina, with the Illumina custom error model used. Rankinvariant-normalized expression data were log10 transformed, and missing data were encoded as missing, rather than as a zero level of expression.</p>
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