GSEA with methylation data
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.9 years ago
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]]
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wenhuo hu ▴ 200
@wenhuo-hu-5208
Last seen 4.2 years ago
United States
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 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]]
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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]]
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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]]
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Wu, Di ▴ 120
@wu-di-4945
Last seen 7.1 years ago
United States
Hi Tim, Th function wilcoxGST in limma package, which is a synonym for geneSetTest with ranks.only=TRUE, will do gene set test for ranks of statistics. In your case, you can put the ranks of t statistics as "statistics". See library(limma) ? wilcoxGST ? geneSetTest Comparing to Hypergeometric tests, Wilcoxon mean rank tests of gene set take care the detail of statistics and require no t statistic cutoff. Both Hypergeometric tests and Wilcoxon mean rank tests assumes genes are independent. Of course, if there are correlations among the genes in the methylation data (I am not sure ...), other functions dealing with correlations, e.g., "roast", "camera", or "romer" in limma may be helpful. This may depend on the distribution of your normalized methylation data. Hope this help. Di ---- Di Wu Postdoctoral fellow Harvard University, Statistics Department Harvard Medical School Science Center, 1 Oxford Street, Cambridge, MA 02138-2901 USA ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] On Behalf Of Tim Smith [tim_smith_666@yahoo.com] Sent: Sunday, May 20, 2012 11:57 AM To: bioc Subject: [BioC] GSEA with methylation data 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]]
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@sean-davis-490
Last seen 12 weeks ago
United States
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? > > Assuming that you might have used limma for differential expression, you could take a look at the roast, romer, and camera functions. Sean > > 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 > [[alternative HTML version deleted]]
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