Hello Davis, I tried using 'de.tgw' instead of 'd' and I got the following error message: > de <- as.logical(abs(decideTestsDGE(de.tgw))) > plotsymbols <- rep(19, nrow(de.tgw)) > plotsymbols[de] <- 4 > plotSmear(de.tgw, cex = 0.8, main="MM Plot", pch=plotsymbols) Error in plotSmear(de.tgw, cex = 0.8, main = "MM Plot", pch = plotsymbols) : Currently only supports DGEList/DGELRT objects as the object argument. Any thoughts on this, will be of great help. Many thanks! Sridhara On Thu, Apr 14, 2011 at 7:44 PM, Davis McCarthy <dmccarthy@wehi.edu.au>wrote: > Hi Sridhara > > Yes, you are right that the error is occurring because you are giving the > decideTestsDGE() function the object 'd' as an argument and 'd' is a DGEList > object. As the error message informs, decideTestsDGE() only works on a > DGEExact or DGELRT object. This is because decideTestsDGE() summarises the > DE status for the genes in your study, so must operate on the results of the > statistical testing procedure for DE. In edgeR these DE results are stored > in either a DGEExact object (produced by exactTest) or a DGELRT object > (produced by glmLRT). > > If you pass your 'de.tgw' object (the one produced by exactTest) to > decideTestsDGE instead of 'd' then you should get what you're after. > > Cheers > Davis > > > > On Apr 15, 2011, at 1:20 AM, Sridhara Gupta Kunjeti wrote: > > Hello Davis, > > Here is the history of the codes: > d <- DGEList(counts = d, group = group) > d > d <- estimateCommonDisp(d) > d <- estimateTagwiseDisp(d, prior.n = 10, grid.length = 500) > prior.n <- estimateSmoothing(d) > prior.n > de.tgw <- exactTest(d, common.disp = FALSE) > de.tgw > sum(de.tgw$table$p.value < 0.01) > sum(de.tgw$table$p.value > 0.01) > detags.tgw <- rownames(topTags(de.tgw, n = sum(de.tgw$table$p.value < > 0.01))$table) > plotSmear(d, de.tags = detags.tgw, main = "FC Plot using tagwise > dispersion") > abline(h = c(-2, 2), col = "dodgerblue", lwd = 2) > plotSmear(d, de.tags = detags.tgw, main = "FC Plot using tagwise > dispersion", cex=0.8, pch=plotsymbols) > plotSmear(d, main = "FC Plot using tagwise dispersion", cex=0.8, > pch=plotsymbols) > de <- as.logical(abs(decideTestsDGE(d))) > Error in decideTestsDGE(d) : Need DGEExact or DGELRT object > > I guess this error message is because all my objects are in DGEList. > Any other code that I could use to get the plot in Black and White with > different shapes for non-DE and DE will be highly appreciated. > > > Thanks, > Sridhara > > > > > On Wed, Apr 13, 2011 at 10:48 PM, Davis McCarthy <dmccarthy@wehi.edu.au>wrote: > >> Hi Sridhara >> >> Remember that all of the usual R plotting commands can be passed to >> plotSmear in the '...' argument (see ?plotSmear). You can just change the >> pch argument as required (the standard R parameter for plotting symbol). >> >> This code is one way of doing what you want to do (assuming that your DE >> results are in a DGEExact or DGELRT object called "results"): >> >> de <- as.logical(abs(decideTestsDGE(results))) >> plotsymbols <- rep(19, nrow(results)) >> plotsymbols[de] <- 4 >> plotSmear(results, cex=0.8, main="MA Plot", pch=plotsymbols) >> >> This will give you closed circles for non-DE genes and 'x's for DE genes. >> You can play with the choice of symbols as you please. >> >> Cheers >> Davis >> >> >> On Apr 13, 2011, at 11:54 PM, Sridhara Gupta Kunjeti wrote: >> >> > Hello, >> > I have used edgeR for DGE analysis and also generated plotSmear. I guess >> by >> > dufault the plotSmear shows red dots for differentially expressed genes. >> > But, I want to generate a black and white plot, is there a possbility to >> > gene using different shape of the points, may be 'x' for the >> differentially >> > expressed genes. If any one know how to change this it will be helpful. >> > >> > Many thanks in advance! >> > Sridhara >> > >> > >> > -- >> > Sridhara G Kunjeti >> > PhD Candidate >> > University of Delaware >> > Department of Plant and Soil Science >> > email- sridhara@udel.edu >> > Ph: 832-566-0011 >> > >> > [[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 >> >> ------------------------------------------------------------------- ----- >> Davis J McCarthy >> Research Technician >> Bioinformatics Division >> Walter and Eliza Hall Institute of Medical Research >> 1G Royal Parade, Parkville, Vic 3052, Australia >> dmccarthy@wehi.edu.au >> http://www.wehi.edu.au >> >> >> ______________________________________________________________________ >> The information in this email is confidential and intended solely for the >> addressee. >> You must not disclose, forward, print or use it without the permission of >> the sender. >> ______________________________________________________________________ >> >> >> >> > > > -- > Sridhara G Kunjeti > PhD Candidate > University of Delaware > Department of Plant and Soil Science > email- sridhara@udel.edu > Ph: 832-566-0011 > > > -------------------------------------------------------------------- ---- > Davis J McCarthy > Research Technician > Bioinformatics Division > Walter and Eliza Hall Institute of Medical Research > 1G Royal Parade, Parkville, Vic 3052, Australia > dmccarthy@wehi.edu.au > http://www.wehi.edu.au > > > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:20}}