[Bioc-devel] annotation package for Affymetrix Hum6000 array

[lgautier at altern.org]

> "James W. MacDonald" <jmacdon at med.umich.edu> writes:
>
>> Laurent Gautier wrote:
>>> My guess is that there is a typo and that chip type is HU6800.
>>
>> No, it isn't a typo. Affy had a chip they called the Hum6000 that had
>> about 6500 probesets on it. Following normal BioC/affy conventions, I
>> would just put hum6000 in the annotation slot.

I did not know (I never heard about that one).

> This is what we've decided to do.

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).


Laurent

>
> Thanks,
>
> + seth
>
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