[BioC] MGU74A and MGU74Av2

[Yongde Bao]

David:

Can you tell us how you dealt with the masked genes in MG 74A with rma?

Thanks, Yongde Bao

At 10:03 AM 6/20/2003 -0700, David O. Nelson wrote:
>Our experience with MGU74A and Av2 chips:
>
>As I recall, the MGU74A and Av2 have a different number of probe sets!
>Also, while there is substantial overlap in affy IDs:
>
>1. there are probe set names in A that are not in Av2 (expected), and
>2. there are probe set names in A2 that are not in A (NOT expected).
>
>We preprocessed the A and Av2 chips separately, because there was some
>confusion in RMA about which CDF environment to use for the A and Av2
>chips.
>
>(I don't recall the details now, and it was never clear whether some
>biologist had edited the CEL file to change the name of the CDF file or
>not.)
>
>In any event, BE CAREFUL when combining v1 and v2 chips!
>
>dave
>
>On Thu, 2003-06-19 at 21:46, Laurent Gautier wrote:
> > On Fri, Jun 20, 2003 at 02:21:51PM +1000, Matthew Hobbs wrote:
> > > Hi,
> > >
> > > I have some cel files from experiments using the Affy MGU74A chip and 
> some
> > > from experiments  using the MGU74Av2 chip.  Am I right in thinking that
> > > MGU74A and MGU74Av2  are actually the same chip described differently
> > > (because some probesets were originally designed wrongly)?
> >
> > I believe that v2 stands for "version 2" which means some improvement
> > was thrown in.
> >
> > >
> > > I wish to treat all this data together.  Can I use theMGU74Av2 CDF to 
> make a
> > > single Affybatch object containing both sorts of data?   If not how 
> should I
> > > proceed?
> >
> > If the differences between those two guys and the ones between U95A and 
> U95v2
> > are comparable, a simple way should be to have an AffyBatch which is the
> > "intersection" between the probe sets in both chips. To achieve this,
> > you will need the probes sequences files (should be available at
> > www.affymetrix.com) and the .CDF files (or corresponding 'cdfenvs').
> > Using these four elements, you will craft a cdfenv that is the intersection
> > of the two others (the functions xy2indices and indices2xy should be handy
> > to shuttle from the x/y coordinates in the sequence files to the indices
> > (NOTE: add 1 to the x/y in the sequence file. The indexing starts at 0
> > in Affymetrix files !!!!!)).
> > If you are lucky, you won't have to shuffle the values in the 'exprs'
> > matrix, but you'd better be prepared to do it...
> >
> >
> > Hopin' it helps,
> >
> >
> > L.
> >
> > _______________________________________________
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> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>--
>David O. Nelson <daven at llnl.gov>
>LLNL
>
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Yongde Bao, Ph.D
Biomolecular Research Facility
Department of Microbiology
University of Virginia School of Medicine
Charlottesville, VA 22908

E-mail: yb8d at virginia.edu
Voice mail: 434-982-2551, 434-924-2553
FAX: 434-982-2514