Dear edgeR community: In the output of edgeR for two groups testing: topTags(et, n=20), for example. We have: Gene ID logFC logCPM pValue FDR I wonder why we only have one column of logCPM, since this is a comparison, I think there should be two such columns, one for each sample? Probably that I misunderstood something here? Thanks, Son. [[alternative HTML version deleted]]

Hi Son, The logCPM is just the overall log average over both groups. So you have the logFC, which tells you how different the two groups were, and the logCPM which tells you the average abundance, which is a way to assess the signal/noise ratio. In other words, the larger the logCPM, the more signal you have and consequently the less influence of noise. Best, Jim On Wednesday, April 09, 2014 2:15:52 PM, Son Pham wrote: > Dear edgeR community: > In the output of edgeR for two groups testing: > topTags(et, n=20), for example. > We have: > Gene ID logFC logCPM pValue FDR > > I wonder why we only have one column of logCPM, since this is a comparison, > I think there should be two such columns, one for each sample? > > Probably that I misunderstood something here? > 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