[BioC] Moderated t-test
Ekta_Jain at jubilantbiosys.com
Wed May 9 08:06:15 CEST 2012
You can use the cbind function.
> toptableOut<- topTable(fit2, number=Inf, adjust.method="BH")$t
> x <- cbind(file[,1],toptableOut)
## the (file[,1] will get you all rows for column 1
> write.table(x,"<filename>.txt", quote=F, row.names=FALSE, sep="\t")
Hope this helps,
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Chintanu
Sent: 09 May 2012 11:21
Subject: [BioC] Moderated t-test
I am trying to do a moderated t-test on two groups of samples as follows -
file <- read.csv (file.choose(), header = TRUE) # Column 1 contains
group <- rep(0:1, c(3,5))
fit <- lmFit(file[,-1], design=group) # Column 1 contains row-names
fit2 <- eBayes(fit)
topTable(fit2, number=Inf, adjust.method="BH")$t
I am not sure how to obtain the values of topTable() along with the
corresponding row names.
Could you please advise.
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