Hello! I am trying to do a boxplot using a subset of a PLMset (just certain boxes). Without trying to subset (3 lines of code below), it works just fine. (It is the same thing as NUSE) # THIS IS OK fplm <- fitPLM(myAffyBatch) ss <- boxplot(fplm) bxp(ss) How can I get a subset of the PLMset ? Here are 2 things that I tried, using the subset argument in boxplot, which did not work (where cels4Plot is a vector containing the CEL file names): ss <- boxplot(fplm, subset = sampleNames(fplm at phenoData)== cels4Plot) ss <- boxplot(fplm, subset = which(sampleNames(fplm at phenoData) %in% cels4Plot)) Thanks for your help!