[BioC] package for pathway analysis

Wolfgang Huber whuber at embl.de
Tue Aug 10 16:32:18 CEST 2010


have a look at the Category, GSEABase, topGO and BioNet packages and in 
particular their vignettes. Check also: Bioinformatics. 2008 Nov 
15;24(22):2586-91. Gene set enrichment analysis using linear models and 
diagnostics. Oron AP, Jiang Z, Gentleman R.

Apologies to everyone I did not mention - there is a lot of good 
literature (and software) on gene set enrichment analysis out there, 
which I will not try to review here, entering "gene set enrichment 
analysis" in Pubmed or Google Scholar would be a good start.

	Best wishes

Dawn scripsit 08/08/10 12:50:
> Hi,
> I have two groups(one is for control) of genomic data and try to do
> metabolic pathway analysis using Bioconductor. Would you please give me some
> suggestion about what packages I should use and the information about how I
> can start (e.g., the tutorial )? I hope to see which genes are up and down
> in particular pathwa*y such as the insulin pathway.*
> *
> *
> *Thank you very much!*
> *Dawn*
> 	[[alternative HTML version deleted]]
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Wolfgang Huber

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