Hello, I am using marrayInput package to import microarray data from different platform sources and I have a couple of doubts about if data are modified and how as the marrayRaw object is created (I'll send separate emails for different questions): - in what form should the maW value be? Is it a numeric value ranging 0:1 or what? In the help I couldn't find any hint about how to use it. In my datafiles there are columns with strings like "DETECTED" or "PASSED" or "LOW_SIGNAL" etc. and I would like to use these informations to flag good or bad spots, such that they are eliminated from subsequent normalization. I have thought to catch these columns with read.marrayInfo and assign maW "good" or "bad" on the basis of it. Also, in some cases I have different indicators for the two channels, so I have to check both to see if the spot is reliable. I am trying something like: #files being the list of datafiles for (i in files) assign(paste("info", i, sep=""), read.marrayInfo(i, info.id=1:22, labels=1)) #and, for each of them, es slide A: Agreen<-maInfo(infoA)[,21] Ared<-maInfo(infoA)[,22] AG<-as.vector(Agreen) AR<-as.vector(Ared) #assuming maW=1 for "good" spots and maW=0 for the "bad" ones Aw<-rep(1, maNspots(data)) Aw[AG=="somewhat-bad"]<-0 Aw[AR=="some-else-bad"]<-0 slot(data, "maW")[,1]<-Aw Is there a better way to do it? Thank you to any that would help me Margherita