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

[Guiyuan Lei]

Hi Jim,

Many thanks. I have checked the s_pombe.msk and s_cerevisiae.msk
files, the overlap between pombe and cerevisiae are probesets which
with prefix "AFFX" and "RPTR". One strange thing is that one probeset
called "177968_at" is in s_pombe.msk but is NOT among the whole 10928
probesets! So the overlap are 152 probesets.

I got one more question, for the Yeast2GENENAME, many probesets only
have ID, but no genename (is "NA"), is it possible to get gene
name/symbol for all 10928 probesets?


Best regards,
Guiyuan

On Nov 28, 2007 2:05 PM, James W. MacDonald <jmacdon at med.umich.edu> wrote:
> 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
> >>>
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor at stat.math.ethz.ch
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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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
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>