dear users of the affy package, we are considering making a change to the pm and mm methods to speed them up (roughly 4 times faster). if this is done pm(affybatch) will return the exact same matrix as before but with no rownames. i personally never use these rownames but i use pm(affybatch) quite often. to get the same rownames you will have to do something like this: pms <- pm(affybatch) rownames(pms) <- probeNames(affybatch) if this will affect anybodies code please let me know. -rafael