[BioC] differential gene set analysis

[Simon Anders]

Hi Ed,

On 04/17/2012 11:45 PM, Ed Siefker wrote:
> Are there tools available for differential gene set analysis?
>
> e.g., if I apply the same treatment to two different cell lines,
> and find gene sets that are enriched in each with respect
> to untreated, can I compare the lists of gene sets and
> find ones that are significantly enriched in one but not
> the other?

Why don't you do it the other way round: First find genes that react 
differently to treatment in cell line 1 than in cell line 2. The do an 
enrichment analysis for these genes.

To find these genes, do a GLM-based analysis testing for interactions 
between cell line and treatment, e.g., with DESeq.

   Simon