[BioC] Moderated t-test

[Gordon K Smyth]

Dear Chintanu,

If you read data including row names, for example,

   y <- read.csv(file.choose(), row.names=1)
   fit <- lmFit(y, design)

then your toptable will automatically include the rownames, and they will 
be correctly sorted.

BTW, your design matrix doesn't make sense to me.

Best wishes
Gordon

> Date: Wed, 9 May 2012 15:51:06 +1000
> From: Chintanu <chintanu at gmail.com>
> To: bioc <Bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Moderated t-test
>
> Hi,
>
> 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
> row-names
>
> 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.
>
> Cheers,
> Chintanu

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