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19 months ago
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Hello! I recently came across decoupleR for transcription factor activity inference in bulk RNA-seq (https://www.bioconductor.org/packages/release/bioc/vignettes/decoupleR/inst/doc/tf_bk.html).
I was wondering why do they use p-values, as opposed to adjusted pvalues, in their analysis of inferring infer pathway activities from the t-values of the DEGs between KO and WT? Is there a specific reason to use raw (unadjusted) pvalues in this context?
Thanks!
Did you find an answer? I’m wondering about the same issue too.
I am specifically interested in p values generated from run_consensus , run_ulm , run_mlm etc.