[BioC] Moderated t-test

Ekta Jain Ekta_Jain at jubilantbiosys.com
Wed May 9 08:06:15 CEST 2012

Hi Chintanu,
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,

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Chintanu
Sent: 09 May 2012 11:21
To: bioc
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))

library (limma)

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.

Thank you.


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