[BioC] Missing probesets

[Malick.PAYE at eu.biomerieux.com]

Hello all,

I installed Bioconductor, the affy package as well as the makecdfenv
package.
I have some problems with package makecdfenv (make.cdf.package function).

I'm working with a custom chip, then I tried to create a CDF package using
my CDF file, when creating and installing the package everything seems to
be ok but when i read my cel files I realise that about 20% of my
probesets are missing.

While trying to track the bug it seems that the missing probesets are
those whose probes are completely/partially included in another probeset ?

So I suppose that the implementation of this package prevents the
inclusion of a probeset in another ?

My question : what can I do to reanalyse my data with the entire
probesets.

I'm not familiar with C language so I can't have a look at the source
code.

PS : I'm using R version 2.0.1, affy version 1.5.8-1 and Makecdfenv :
version: 1.4.8

If someone met this kind of problem. ..

Any help would be greatly appreciate.

Malick,

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