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

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