Dear Bioconductor, I have a question about how to derive the gene centric values for the probe set: When reading the paper I saw this description: "From the methods (Microarray Experiments): “Probes on all three platforms were aligned to a transcript database consisting of RefSeq (36.1) and complete coding sequences from GenBank (v.161). Gene centric expression values were generated for every gene with at least five perfect-match probes (Affymetrix).” Practically speaking, we use a CDF which combined the probes as described above, in combination with the aroma.affymetrix R library. Similar CDFs can be obtained from the AffyProbeMiner website." Does anyone has an example of the aroma.affymatrix code or could tell me which command to use to implement this? Thanks a lot. best, xiaowei [[alternative HTML version deleted]]