Gwilymh, the q value was replaced with a Benjamini-Hochberg false discovery rate correction. This is in the criteria.we.BH column
ALDEx 2 is not returning q-values
質問
I am analyzing RNA-Seq data in ALDEx 2 (http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0067019#s3). For some reason, the table of the final results is missing it's q-values. My code is below, as are the first 4 lines of output. Any suggestions as to what is (not) happening?
Code:
data<-read.table("M_ARxCH.txt",sep="\t", header=T,stringsAsFactors=T,row.names=1)
cond<-c("AR","AR","AR","CH","CH","CH")
ARxCH<-aldex(data,cond,mc.samples=256)
ARxCH_Sum<- summary.aldex(ARxCH)
Output:
rab.all.q50 rab.win.AR.q50 rab.win.CH.q50 diff.btw.q50 diff.win.q50 effect.q50 criteria.we.pval criteria.we.lfdr criteria.we.BH criteria.wi.pval criteria.wi.lfdr criteria.wi.BH
FBgn0012691 1 1 2 1 6 0 0.71 0.735 0.759 0.705 1 0.979
FBgn0012692 0 0 1 0 6 0 0.577 0.256 0.662 0.907 1 0.993
FBgn0020474 -6 -6 -6 1 2 0 0.451 0.345 0.701 0.554 1 0.905
According to the manual, there should be a column labelled criteria.we.qval between criteria.we.pval and criteria.we.lfdr
正しい解決策はありません
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