[BioC] limma: get all sig genes from multiple contrasts

[James W. MacDonald]

Hi Ivan,

Ivan Baxter wrote:
> Thanks Jim- that will help  I think I am still going to get useful 
> information out of the clustering. I have 7 different combinations of 
> treatments, so the number of different patterns is going to be quite 
> large. Clustering seems to be  a good way to get a feel for which 
> patterns are there and  of interest. For a package like goCluster, 
> wouldn't I want to reduce the number of genes which are in the set that 
> is analyzed (say from 22k to ~1k)? While there might be genes that fit a 
> certain pattern that isn't significantly different in any of my 
> contrasts, it seems likely that it would be in the minority. After I 
> have identified interesting patterns from the significantly changed 
> genes, I could then go back in and see if other genes match that pattern?

Using goCluster is a slightly different subject, because you are 
clustering based on the GO terms rather than the expression values. In 
that case I don't think it is a problem to select genes in this manner.

Best,

Jim




-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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