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

James W. MacDonald jmacdon at med.umich.edu
Fri Jun 9 21:47:14 CEST 2006

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.



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

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

More information about the Bioconductor mailing list