The simplest thing might just be to use the 'regulatory features' column in the 450k annotations (for the subset of 27k probes carried over) and do hypergeometric tests for each. I'll re-post an old example with these included and modified for 27k. On Sun, May 20, 2012 at 9:01 AM, wenhuo hu <huwenhuo@gmail.com> wrote: > Hi > > Would you check this? > > > http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Da ta_formats#Ranked_Gene_Lists > > On my way to outside, nice sun today. > > Wen > > On Sun, May 20, 2012 at 11:57 AM, Tim Smith <tim_smith_666@yahoo.com> > wrote: > > > Hi, > > > > I wanted to conduct GSEA analysis on methylation data (illumina 27k). > > After conducting a differential analysis, I have a list of genes along > with > > their pvalues and t-statistics. Is there a way that I can conduct a GSEA > > analysis with this data? Which packages should I be looking at? > > > > > > I have looked at a few of the GSEA packages, but they all seem to be > based > > on gene expression data (and chips/annotation packages etc.). > > > > thanks! > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > > > Wenhuo Hu > Park lab > > Memorial Sloan Kettering Cancer Center > Zuckerman Research Building > 408 East 69th Street > Room ZRC-527 > New York, NY 10065 > Phone 646-888-3220 > huw@mskcc.org > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]

Hi Wen, Thanks for the reply! Do you know a bioconductor package that will do what the Broad GSEA tool does? thanks! ________________________________ From: wenhuo hu <huwenhuo@gmail.com> Cc: bioc <bioconductor@stat.math.ethz.ch> Sent: Sunday, May 20, 2012 12:01 PM Subject: Re: [BioC] GSEA with methylation data Hi Would you check this? http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data _formats#Ranked_Gene_Lists On my way to outside, nice sun today. Wen Hi, > >I wanted to conduct GSEA analysis on methylation data (illumina 27k). After conducting a differential analysis, I have a list of genes along with their pvalues and t-statistics. Is there a way that I can conduct a GSEA analysis with this data? Which packages should I be looking at? > > >I have looked at a few of the GSEA packages, but they all seem to be based on gene expression data (and chips/annotation packages etc.). > >thanks! > >       [[alternative HTML version deleted]] > > >_______________________________________________ >Bioconductor mailing list >Bioconductor@r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Wenhuo Hu Park lab Memorial Sloan Kettering Cancer Center Zuckerman Research Building 408 East 69th Street Room ZRC-527 New York, NY 10065 Phone 646-888-3220 huw@mskcc.org [[alternative HTML version deleted]]