Hi Roulin, Please ask the forum and not personally. As I mentioned there aretwo ways of doing it, Either by extracting the MM nad PM values for each of the probes from a probe-set, or by summarizing the intensity values without normalizing it. As I wanted one value for each gene, I have chosen the second option. For that you can use the expresso command, were you set bg.correct and normalize as FALSE. You than need to choose a pm.correct method and the summarization method you prefer. This will give you a table of values for each of the genes and arrays you are using in an affyBatch (input). Hope this helps Assa On Wed, Apr 18, 2012 at 07:19, Ruolin Liu <ruolin@iastate.edu> wrote: > Hi Assa, > > I am facing the same problem you came across before: For each probe, how > to extract intensity values along with the probe name from CEL file using > R. I am haunted by it for quite a while. Could you please tell me the way > in which you settle it down or, if possible, copy and paste your code. I'll > appreciate your help. > > Thanks for your time, > > Ruolin Liu > [[alternative HTML version deleted]]