Hi, Can you please tell me how the FC is calculated in the following test in edgeR? DrugvsPlacebo.1h = (Drug.1h-Drug.0h)-(Placebo.1h-Placebo.0h), Lana Schaffer The Scripps Research Institute Biostatistics, Informatics DNA Array Core Facility 858-784-2263 [[alternative HTML version deleted]]

Hi Lana, The fold change (actually log2 fold change) for a contrast is simply the sum/difference of all the coefficients in the contrast as you have written it. So if Drug.1h, Drug.0h, Placebo.1h, and Placebo.0h are 4 coefficients in your model, then your "DrugvsPlacebo.1h" contrast works out to: 1 * Drug.1h + -1 * Drug.0h + -1 * Placebo.1h + 1 * Placebo.0h The logFC for each gene is computed by substituting the fitted values for each coefficient into the expression that you specify as the contrast. -Ryan On Fri 17 Jan 2014 01:08:51 PM PST, Lana Schaffer wrote: > Hi, > Can you please tell me how the FC is calculated in the following test in edgeR? > DrugvsPlacebo.1h = (Drug.1h-Drug.0h)-(Placebo.1h-Placebo.0h), > > Lana Schaffer > The Scripps Research Institute > Biostatistics, Informatics > DNA Array Core Facility > 858-784-2263 > > > [[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