[BioC] GSEA

[Martin Morgan]

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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