[BioC] Limma with common Reference Design

[michael watson (IAH-C)]

Hi Sean

I want to do in limma what I would have normally done using mt.teststat
in the multtest package - that is perform a moderated t-test for each
row of my data, testing for the difference between the two groups (where
one group is T1/Ref and the other is T2/Ref), adjusting for the FDR.  It
looks like I do need the contrasts matrix, and the coefficient of
interest is T1-T2.

So If I use design matrix

	T1	T2
1	0	1
2	0	1
3	0	1
4	1	0
5	1	0
6	1	0

And a contrasts matrix so:
	T1	T2	T1-T2
T1	1	0	1
T2	0	1	-1

Then lmfit(), eBayes and topTable, as in the user guide, that's the
limma equivalent of a moderated t-test for each row as described above?

Cheers
Mick

-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
Sent: 08 October 2004 17:31
To: michael watson (IAH-C)
Cc: Bioconductor
Subject: Re: [BioC] Limma with common Reference Design



On Oct 8, 2004, at 10:57 AM, michael watson (IAH-C) wrote:

>
> Is this right?  From reading the examples, I think it is, but I am not

> sure what the advantage is of having the contrasts matrix as well as 
> the design matrix, adding the contrasts matrix certainly gives me 
> different results to just using the design matrix alone.  Hmmmmm.
>

Mick,

The answer depends on what you want to get?  I am assuming that you 
actually want to have T1-T2, so you do need the contrast matrix.  You 
don't get that quantity directly from the design matrix, so there is no 
comparable answer using a design matrix alone as compared to including 
a contrast matrix.  The first two coefficients for each should be the 
same, though.

Sean