Hi, I have a scatterplot of 2 chips against each other. Now my problem is .. I have a list of affyids, which I want to plot in a different colour(say red) on this scatterplot. How do I go about doing this? I searched the list archives, but got nothing! Sorry, if it is a too simplistic question. thanks, V [[alternative HTML version deleted]]

vasantika s wrote, On 09.04.2009 12:10: > Hi, > > I have a scatterplot of 2 chips against each other. Now my problem is .. > > I have a list of affyids, which I want to plot in a different colour(say > red) on this scatterplot. How do I go about doing this? > > I searched the list archives, but got nothing! Sorry, if it is a too > simplistic question. > > thanks, > V Hi V, assuming that eset is an ExpressionSet object and affy.ids a vector of Affy probesets, this will do it: > plot(exprs(eset[, 1]), exprs(eset[, 2])) > points(exprs(eset[affy.ids, 1]), exprs(eset[affy.ids, 2]), col="red") You might want to change 1 and 2 to some of your sample names. HTH, Christof -- Christof Winter Bioinformatics Group Biotechnologisches Zentrum Technische Universit?t Dresden Tatzberg 47-51 01307 Dresden Germany