[BioC] Filter out pombe probeset from cerevisiae probesets for yeast2 Affymetrix chip

[James W. MacDonald]

Hi Guiyuan,

Guiyuan Lei wrote:
> Thank Jim and Caroline,
> 
> I found that there are 5749 probesets in s_pombe.msk and  5028
> probesets in s_cerevisiae.msk while there are total 10928 probesets on
> yeast2 chip. Does it mean that there are overlap between pombe and
> cerevisiae probesets?

Probably. The 151 unmasked probesets are too many to simply be the 
control probesets, but the only way to know for sure is to read Affy's 
documentation, and if that doesn't help, then contact Affy.

> 
> By the way, is there any smart way to use s_cerevisiae.msk to hide
> pombe probesets in cdf environment, i.e. use s_cerevisiae.msk as
> argument of some function so that R can only read cerevisiae probesets
> when do analysis?

Take a look at the altcdfenvs package.

Best,

Jim


> 
> Best regards,
> Guiyuan
> 
> On Nov 27, 2007 9:05 PM, Caroline Lemerle <caroline.lemerle at gmail.com> wrote:
>> Hi Guiyuan,
>>
>> I don't see it either but exactly that information is available for
>> download on the manufacturer's website, here:
>>
>> http://www.affymetrix.com/Auth/support/downloads/mask_files/s_cerevisiae.zip
>> http://www.affymetrix.com/Auth/support/downloads/mask_files/s_pombe.zip
>>
>> file x contains the list of probesets from organism x on the yeast2 chip.
>>
>>
>>
>> On Nov 27, 2007 7:16 PM, Guiyuan Lei <guiyuanlei at gmail.com> wrote:
>>> Dear all,
>>>
>>> I am analyzing microarray data for Affymetrix yeast2 chip, I know that
>>> there are two organisms pombe and cerevisiae on this chip. I need to
>>> filter out pombe probesets. There are total 10928 probesets on yeast2
>>> chip. How can I know which probeset is corresponding to pombe and
>>> which probeset is corresponding to cerevisiae?
>>>
>>> (1)  I could get a list of probeset ID and genename from library
>>> "yeast2" (R command: as.list(yeast2GENENAME)), that is 6356 probesets.
>>>  Are these 6356 probesets Cerevisiae probesets?
>>> (2) After I updated Bioconductor today, I found that the
>>> "yeast2GENENAME" contains total 10928 probesets! In latest version of
>>> Bioconductor, all probesets on yeast2 chip are included in
>>> "yeast2GENENAME", but there is no information about  which probeset is
>>> pombe and which one is cerevisiae. Is there any new library/function
>>> which I can use to separate these 10928 probesets into cerevisie
>>> probesets and pombe ones?
>>>
>>> Many thanks!
>>>
>>> Best regards,
>>> Guiyuan
>>>
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623