Hi, I have done RNA-Seq using cuffdiff, edgeR, and Partek software And get a different list of differential expressed transcripts For all the software. Has anyone have any comments about this? Lana Schaffer Biostatistics, Informatics DNA Array Core Facility 858-784-2263 [[alternative HTML version deleted]]

It is very difficult to compare all thes results. Perhaps best is you may like to decide first what is the purpose of your study and choose the analysis. If you can confirm in the downstream analysis, that should be it. Partek and Cuffdiff uses a totally different approach. Best. --- On Fri, 10/14/11, Lana Schaffer <schaffer@scripps.edu> wrote: From: Lana Schaffer <schaffer@scripps.edu> Subject: [BioC] RNA-Seq : comparison cuffdiff, edgeR, Partek To: "'bioconductor@r-project.org'" <bioconductor@r-project.org> Date: Friday, October 14, 2011, 1:59 AM Hi, I have done RNA-Seq using cuffdiff, edgeR, and Partek software And get a different list of differential expressed transcripts For all the software. Has anyone have any comments about this? Lana Schaffer Biostatistics, Informatics DNA Array Core Facility 858-784-2263     [[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]]