Hello,
I am not only interested in finding out which genes are the most highly up- or down-regulated (which I have done using the linear models and Bayesian statistics in Limma), but I also want to know which genes are consistently highly transcribed (ie. they have a high intensity in the channel of interest eg. Cy5 or Cy3 across the set of experiments). I might have missed a straight forward way to do this, or a valuable function, but I've been using my own methods and going around in circles. So far I've normalized within and between arrays, then returned the RG values using RG<-RG.MA, then I ranked each R and G values for each array as below. rankRG<-RG rankRG$R[,1]<-rank(rankRG$R[,1]) rankRG$R[,2]<-rank(rankRG$R[,2]) .. and so on for 6 columns(ie. arrays, as well as the G's) then I thought I could pull out a subset of rankRG using something like; topRG<-rankRG topRG$R<-subset(topRG$R,topRG$R[,1]<500&topRG$R[,2]<500&topRG$R[,5]<500) However, this just returned me a matrix with one row of $R (the ranks were <500 for columns 1,2, and 5 and greater than 500 for 3,4,and 6). However, I can't believe that there is only one gene that is in the top 500 for R intensitiy among those three arrays. Am I doing something wrong? Can someone think of a better way of doing this? Thanks Alison ****************************************** Alison S. Waller M.A.Sc. Doctoral Candidate [EMAIL PROTECTED] 416-978-4222 (lab) Department of Chemical Engineering Wallberg Building 200 College st. Toronto, ON M5S 3E5 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.