Dear all, In the last few weeks, I came across a specific question several times: Which cdf is the most common/complete/appropriate for gene level arrays? I know that the one-to-one mapping of probes to probesets is not valid any more for these arrays. Hence you will lose some genes building your own cdf environment via make.cdf.package. Of course, there is the alternative of using the xps package which uses pgf and clf files. however I am not sure how xps resolves the mapping problem. Additionally, there is the custom cdf option (e.g. brainarray) which offers completely redefined probesets but again you will lose many probes. I think there must be people around, who analyze these arrays quite frequently and must have more insight. So I wondered if a standard procedure has been established or if everybody just tries to find the optimal solution for his own specific experiment. Best, Stefanie [[alternative HTML version deleted]]