[Bioc-devel] annotation package for Affymetrix Hum6000 array

lgautier at altern.org lgautier at altern.org
Thu May 4 17:26:51 CEST 2006

> lgautier at altern.org writes:
>> Since we are about Affymetrix chips and data, apparently there is a
>> quirk
>> with the example data in 'affydata' and the corresponding probe sequence
>> package (the probe sets in the AffyBatch does not seem to match the
>> probe
>> sequences).
>> I am not sure this is a big deal, but it might be handy to know for the
>> people having code dealing with Affymetrix probe sequence and having
>> examples for it
>> (for example, it makes some of example in 'affypdnn' examples behave
>> erratically).
> Can you give a bit more detail or an example?

Sorry for the delay. I get a zillion things to do those days.

When running the example for 'find.params.pdnn'
- the parameters Ns are strangely negative (while they are positive with
"real" data.
- if the parameter give.warnings is set to TRUE, there are a "apparently"
problems catched by the function (I say "apparently", since the routine
itself could be catching things that are not problems.

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