Dear Bioconductors, I would like to generate a scatter plot of single colour array data where; 1) up-regulated genes with FDR <= 0.05, points are coloured in red 2) down-regulated genes with FDR <= 0.05, points are coloured in blue 3) all other points are in green/other colour I know I can do volcano straight from Limma but a simple scatter plot with colours would be useful. Thanks. [[alternative HTML version deleted]]

Sorry if this appears more than once, I have not been recieving any bioconductor mails, so I re-joined (after unsubscribing) Dear Bioconductors, I would like to generate a scatter plot of single colour array data where; 1) up-regulated genes with FDR <= 0.05, points are coloured in red 2) down-regulated genes with FDR <= 0.05, points are coloured in blue 3) all other points are in green/other colour I know I can do volcano straight from Limma but a simple scatter plot with colours would be useful. Thanks. [[alternative HTML version deleted]]

library(lattice) xyplot(fc ~ grp1,data=toplot,groups=res,xlab="Log2 Intensity",ylab="Log2 Fold Change",auto.key=list(text=c("down","not","up"))) toplot contains the intensity (e.g grp1) and foldchange (as e.g. obtained by limma's topTable) and res is the result as obtained by limma's decideTests for the contrast you use. toplot: grp1 grp2 fc res Georg On 31 May 2011 16:13, john herbert <arraystruggles at="" gmail.com=""> wrote: > ?Dear Bioconductors, > I would like to generate a scatter plot of single colour array data where; > > 1) up-regulated genes with FDR <= 0.05, points are coloured in red > 2) down-regulated genes with FDR <= 0.05, points are coloured in blue > 3) all other points are in green/other colour > > I know I can do volcano straight from Limma but a simple scatter plot with > colours would be useful. > > Thanks. > > ? ? ? ?[[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 >