[BioC] equivalent probes between microarray platforms

[Sean Davis]

----- Original Message -----
From: "Robert Gentleman" <rgentlem at jimmy.harvard.edu>
To: "Benjamin Haibe-Kains" <bhaibeka at ulb.ac.be>
Cc: "Bioconductor Mailing List" <bioconductor at stat.math.ethz.ch>
Sent: Friday, October 15, 2004 3:52 PM
Subject: Re: [BioC] equivalent probes between microarray platforms


> On Fri, Oct 15, 2004 at 06:06:39PM +0200, Benjamin Haibe-Kains wrote:
> > Hi all,
> >
> > I would want to compare results from different article using different
> > micrarray platforms:
> >
> >     1. I have experiments hybridized on the Affymetrix hgu133plus2 and i
> > want to compare them against those from affymetrix hu6800 chip.  In the
> > Affymetrix website, I have not found the probes equivalent on the two
> > platforms in the array comparison spreadsheets. I have the unigene
> > cluster id and the genbank accession number for these probes ... How can
> > I safely find the equivalent probes ?
>
>
>   matchprobes, has for some number of years now ,provided this
>   functionality.
>
> >
> >     2. I have the same problem to resolve but from the Affy hgu133plus2
> > chip and a specific cDNA platform. Again I have trhe unigene cluster id
> > and the genbank accession number.
> >
>   there are many issues here, you can do some sequence matching. You
>   might alow want to look at, since just matching probes is not always
>   the best thing to do.

You might want to look at the mergemaid package for the latter problem.

Sean