[BioC] using GSEABase objects to perform GSEA

[Martin Morgan]

Hi Burak --

GSEABase is meant to provide infrastructure for gene-set based
operations, rather than implementations of gene set enrichment
algorithms.

The PGSEA package might be a useful direction to explore (with or
without GSEABase -- you could use getBroadSets to retrieve predefined
gene sets, feed GeneSetCollections into the PGSEA function, or use
GeneSet objects to subset an ExpressionSet, for instance).

There are differing opinions about what constitutes gene set
enrichment analysis; for one view see the slides from the recent
Bioconductor workshop in Chicago, e.g., GSEA07.pdf or Category.R;
available from

http://daisy.prevmed.northwestern.edu/~denise/BiocChicago2007/

or by navigating from bioconductor.org -> workshops tab.

Hope that helps,

Martin


burak kutlu <burak_kutlu at yahoo.com> writes:

> I am looking at the GSEABase vignette on how to create GeneSets.
> I was wondering if there is an example of how to use these sets to perform the actual GSEA analysis. 
> Thanks in advance
> -burak
>
>
>
> __________________________________________________
>
>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor