Dear all, I am a novice edgeR user. The edgeR manual describes the steps to produce an maPlot from 2 groups of samples, page 5/58 in: http://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc /edgeR.pdf par(mfrow = c(1, 2)) maPlot(D[, 1], D[, 2], normalize = TRUE, pch = 19, cex = 0.2, ylim = c(-8, 8)) grid(col = "blue") abline(h = log2(f[2]), col = "red", lwd = 4) maPlot(d$counts[, 1]/d$samples$lib.size[1], d$counts[, 2]/d$samples$lib.size[2], normalize = FALSE, pch = 19, cex = 0.2, ylim = c(-8, 8)) grid(col = "blue") I suspect that the commands plot samples 1 and 2 and NOT groups 1 and 2. Am I correct? What can I do to actually look at group comparisons? Thanks, Iddo [[alternative HTML version deleted]]

Hi Iddo. Have a look at the plotSmear() function (see page 46 of the user's guide, for example). Cheers, Mark On 2010-09-12, at 9:40 PM, Iddo Ben-Dov wrote: > Dear all, > > I am a novice edgeR user. > > The edgeR manual describes the steps to produce an maPlot from 2 groups of samples, page 5/58 in: > http://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/d oc/edgeR.pdf > > par(mfrow = c(1, 2)) > maPlot(D[, 1], D[, 2], normalize = TRUE, pch = 19, cex = 0.2, ylim = c(-8, 8)) > grid(col = "blue") > abline(h = log2(f[2]), col = "red", lwd = 4) > maPlot(d$counts[, 1]/d$samples$lib.size[1], d$counts[, 2]/d$samples$lib.size[2], normalize = FALSE, pch = 19, cex = 0.2, ylim = c(-8, 8)) > grid(col = "blue") > > > I suspect that the commands plot samples 1 and 2 and NOT groups 1 and 2. > Am I correct? > What can I do to actually look at group comparisons? > > Thanks, > Iddo > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}