Question

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

No correct solution

OTHER TIPS

Gwilymh, the q value was replaced with a Benjamini-Hochberg false discovery rate correction. This is in the criteria.we.BH column

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