Hi all, I have a question about GSEA analysis. There is an item about phenotype lable in Java version GSEA, it is about the .cls data, with an extension, e.g. "WT~KO", or "KO~"WT". I tried both way, the results are quite different. The way described in the original paper on how GSEA works does not seem give an excuse how this parameter affect the results, and why this happened. Please help! Wenhuo Hu, MSKCC [[alternative HTML version deleted]]

This isn't really a Bioconductor question, but for general bioinformatics questions you can try Biostar: http://biostar.stackexchange.com/ Paul. On Fri, Apr 6, 2012 at 12:49 PM, wenhuo hu <huwenhuo@gmail.com> wrote: > Hi all, > > I have a question about GSEA analysis. There is an item about phenotype > lable in Java version GSEA, it is about the .cls data, with an extension, > e.g. "WT~KO", or "KO~"WT". I tried both way, the results are quite > different. The way described in the original paper on how GSEA works does > not seem give an excuse how this parameter affect the results, and why this > happened. Please help! > > Wenhuo Hu, > MSKCC > > [[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 > -- Paul Geeleher (PhD Student) School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com [[alternative HTML version deleted]]