Hi, I have just extracted out the hgu95av2probe$sequences and got 19,9084 but have 201800 intensities from a HGU95av2 CEL file. Have you seen this discrepancy before? perhaps the CEL file is mislabeled? Lana [[alternative HTML version deleted]]

Hi Lana, the probe packages correspond 1:1 to Affymetrix's "probe_tab" files. They typically do not contain sequences for all probes on the array (e.g. some control probes or "empty" cells would be expected to miss). You will need to take care of the mapping between rows of the hgu95av2probe$sequences table and rows of the AffyBatch. The functions i2xy and xy2i (in the arehgu95av2cdf package) or equivalently sxy2indices and indices2xy (in the package affy) are supposed to help you with that. Does this help? Best regards Wolfgang Schaffer wrote: > Hi, > I have just extracted out the hgu95av2probe$sequences and got 19,9084 but > have 201800 intensities from a HGU95av2 CEL file. Have you seen this > discrepancy before? perhaps the CEL file is mislabeled? > Lana ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber