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

[James W. MacDonald]

Hi Guiyuan,

Download the Affy mask file:

http://www.affymetrix.com/Auth/support/downloads/mask_files/s_cerevisiae.zip

Then you can read in the s_cerevisiae.msk file using read.table() and 
subset your data accordingly.

Best,

Jim



Guiyuan Lei 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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-- 
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