[BioC] package for pathway analysis

mkbehnke at gmail.com mkbehnke at gmail.com
Tue Aug 10 21:19:19 CEST 2010


I also like the package 'pcot2' written by Sarah Song. It checks all KEGG pathways by default but you can, with a little elbow grease, define your own genesets to test as well. I like it better the GSEA etc because it is a true multivariate test (Hotellings T-square)

Martha

Sent from my Verizon Wireless BlackBerry

-----Original Message-----
From: Wolfgang Huber <whuber at embl.de>
Sender: bioconductor-bounces at stat.math.ethz.ch
Date: Tue, 10 Aug 2010 16:32:18 
To: <bioconductor at stat.math.ethz.ch>
Subject: Re: [BioC] package for pathway analysis

Dawn,

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
	Wolfgang


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]]
>
> _______________________________________________
> 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


-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber

_______________________________________________
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


More information about the Bioconductor mailing list