[Bioc-devel] annotation package for Affymetrix Hum6000 array

Hi,

I am improving the experimental data set colonCA, which contains the data 
from  Alon et al. (1999, PubMed: 10359783).  I am trying to figure out 
what should be put in the "annotation" slot of the exprSet object for such 
data.  According to Alon 1999, they were using Affymetrix Hum6000 array, 
but I cannot find it in either Affymetrix website or BioConductor 
website.  Does anyone have ideas about what it is and what we should put 
in the annotation slot?  

Thanks,
Ting

My guess is that there is a typo and that chip type is HU6800.

On Tue, Apr 25, 2006 at 10:08:13AM -0700, Ting-Yuan Liu wrote:

Hi,

I am improving the experimental data set colonCA, which contains the data 
from  Alon et al. (1999, PubMed: 10359783).  I am trying to figure out 
what should be put in the "annotation" slot of the exprSet object for such 
data.  According to Alon 1999, they were using Affymetrix Hum6000 array, 
but I cannot find it in either Affymetrix website or BioConductor 
website.  Does anyone have ideas about what it is and what we should put 
in the annotation slot?  

Thanks,
Ting

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.

"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.

This is what we've decided to do.

Thanks,

+ seth

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).