Dear Gordon,

Thank you - I was not sure but had a feeling that the way I was doing it,
it would give inconsistent outcome at the end while trying to retrieve the
row names corresponding to the outcomes using functions like cbind().

Re the design, I have two groups of samples (each group having 3 and 5
samples respectively), and am interested in applying lmFit (). Please
rectify me if I am making any error here.

Best,
Chintanu

=============================================================

On Thu, May 10, 2012 at 4:14 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> 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@gmail.com>
>> To: bioc <Bioconductor@stat.math.ethz.**ch<Bioconductor@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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