[BioC] matching expression profiles

Lana Schaffer schaffer at scripps.edu
Mon Jan 14 18:33:29 CET 2008

I am just asking about the expression of a single gene across all the
I have been reminded that genefinder would be a for me and I have used
it before.

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Monday, January 14, 2008 9:25 AM
To: Lana Schaffer
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] matching expression profiles

Hi Lana,

What exactly do you mean by 'expression profiles'?

If you mean e.g., person A says these 100 genes are interesting in the
experimental system I am investigating, and I want to compare my results
to hers, then I think you want to use GSEA.

I am most familiar with the variant in the Category package, but you
might also consider PGSEA or GSEAbase, depending on where your
expression profile comes from.



Lana Schaffer wrote:
> Friends,
> What packages would you recommend in Bioconductor that would match 
> expression profiles similar to a given expression profile and perhaps 
> draw them ?
> Thanks,
> Lana Schaffer
> 	[[alternative HTML version deleted]]
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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

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