[BioC] GSEA ???

[Loren Engrav]

Thank you

Our question I think will be rather "simple"

We have porcine Affy GeneChip data from Duroc/Yorkshire deep/shallow wounds
over time and will just ask if any gene sets are enriched in this data

Will probably give them all a try unless you suggest one is clearly "better"

Thank you


> From: Martin Morgan <mtmorgan at fhcrc.org>
> Date: Sun, 23 Nov 2008 12:10:32 -0800
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] GSEA
> 
> Loren Engrav <engrav at u.washington.edu> writes:
> 
>> Greetings
>> 
>> There is the GSEABase in Bioconductor
> 
> GSEABase provides infrastructure for managing sets of genes, and for
> mapping between identifiers; it doesn't 'do' a gene set enrichment
> analysis. Also, the GSEABase infrastructure came after other R-based
> GSEA-like packages and so it may be a bit less useful for what it's
> named after than its name suggests.
> 
> GSEA-like analyses in R include PGSEA, Category, GSEAlm, and probably
> others. The reasons to choose between these and non-R tools is likely
> to be driven by suitability of analysis for question at hand.
> 
> Martin
> 
>> But there is also the GSEA located at www.broad.mit.edu/gsea/
>> 
>> For a newbie to GSEA, is there any reason(s) to begin with one or the other?
>> 
>> Thank you
>> 
>> -- 
>> Loren Engrav, MD
>> Univ Washington
>> Seattle
>> 
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> 
> -- 
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
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> 
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