[BioC] gene set enrichment

[Steve Lianoglou]

Hi Gordon,

When an expert comments on a topic I'm interested in, it's hard for me
not to press for more insight so I hope you don't mind, but also ...
you know .. take your time :-)

On Sat, Dec 1, 2012 at 8:39 PM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
[snip]
> The term "gene set enrichment analysis" was coined by the Broad Institute:
>
>   http://www.broadinstitute.org/gsea/
>
> but you certainly can't simply give a list of genes to GSEA.  It requires
> complete data and is designed for microarrays rather than RNA-Seq anyway.

I'm curious if you say so because GSEA doesn't account for something
like length bias? The GSEA folks seem to suggest that one could do
this like any other "pre-processed" GSEA analysis by simply providing
a ranked list of genes (presumably by fold-change):

http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/FAQ#Can_I_use_GSEA_to_analyze_SNP.2C_SAGE.2C_ChIP-Seq_or_RNA-Seq_data.3F

Would you mind (briefly) elaborating a bit on why you disagree?

Thanks,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact