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Labels of Cond1type and Cond2type were swapped in HTSeq data example of DEA? #1

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ianyfchang opened this issue Nov 2, 2018 · 0 comments
Open

Labels of Cond1type and Cond2type were swapped in HTSeq data example of DEA? #1

ianyfchang opened this issue Nov 2, 2018 · 0 comments

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@ianyfchang
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In the example: HTSeq data: Downstream analysis BRCA
mat1 was tumor, mat2 was normal, but the Cond1type was normal, and the Cond2type was tumor.

dataDEGs <- TCGAanalyze_DEA(mat1 = dataFilt[,dataSmTP_short], mat2 = dataFilt[,dataSmNT_short], Cond1type = "Normal", Cond2type = "Tumor", fdr.cut = 0.01 , logFC.cut = 1, method = "glmLRT")

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