Hi All, Could you let me know what is the default value (or recommended value) for thresholding the FDR in edgeR? Thanks, Son. [[alternative HTML version deleted]]

Hi Son, If I understand your question correctly, there is no default. In other words, if you look at the api for topTags, you see: topTags(object, n=10, adjust.method="BH", sort.by="PValue") and there isn't anything there to threshold the results by FDR. However, you can use decideTestsDGE: decideTestsDGE(object, adjust.method="BH", p.value=0.05) which will allow you to select an FDR (or other (un)adjusted p-value) on which to threshold, or you can use the default of 0.05. Best, Jim On Wed, Sep 3, 2014 at 12:46 AM, Son Pham <spham at="" salk.edu=""> wrote: > Hi All, > Could you let me know what is the default value (or recommended value) for > thresholding the FDR in edgeR? > Thanks, > Son. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]