From e34e7da50fc0ff5ed41e8bdaf2b1d41c9e9cf534 Mon Sep 17 00:00:00 2001 From: Bonface Date: Thu, 15 Feb 2024 06:09:54 -0600 Subject: Update dataset RTF Files. --- general/datasets/GSE15222_F_N_RI_0409/platform.rtf | 5 ----- 1 file changed, 5 deletions(-) delete mode 100644 general/datasets/GSE15222_F_N_RI_0409/platform.rtf (limited to 'general/datasets/GSE15222_F_N_RI_0409/platform.rtf') diff --git a/general/datasets/GSE15222_F_N_RI_0409/platform.rtf b/general/datasets/GSE15222_F_N_RI_0409/platform.rtf deleted file mode 100644 index 5bcda8b..0000000 --- a/general/datasets/GSE15222_F_N_RI_0409/platform.rtf +++ /dev/null @@ -1,5 +0,0 @@ -

Illumina Human 50 mer probes. Total of 24357 probes according to Myers et al. A total of 24354 probes included in this GeneNetwork file.

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From the Methods section of the paper:

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Genotyping and Expression Profiling 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 profiles 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.

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