[BioC] limma

[Gordon K Smyth]

> Date: Mon, 24 Jan 2005 15:39:57 +0000
> From: Josephine <josephine.brennan at ucd.ie>
> Subject: [BioC] limma
> To: bioconductor at stat.math.ethz.ch
>
> Hi everyone,
> I have a question concerning spotted array analysis and limma.
> The analysis is working fine except I'm not sure what the out put means.
> I have sample A and samlpe B on an array (3 replicate slides) and in limma analysis I put sample A
> as the reference.
>  Therefore the results I get, are they the genes up/down regulated due to sample A or sample B?
> Josephine Brennan

Positive M-value in toptable means up in sample B, negative means down in sample B.

That makes sense since you have specified sample A to your reference and hence sample B to be the
test sample -- positive means up relative to the reference, negative means down relative to the
reference.

Gordon