[BioC] Match the probe sets from three microarray platforms

Sean Davis sdavis2 at mail.nih.gov
Fri Dec 30 12:47:44 CET 2005

On 12/29/05 7:24 PM, "weinong han" <hanweinong at yahoo.com> wrote:

> Hi, lists,
>   Happy New Year!
>   I have different gene lists from three microarray platforms. Now, I want to
> match the probes from the three platforms by using accession numbers or by
> using Unigene Cluster ID and gene names provided by Affymetrix(HG-U133A and
> HG-U95av2) and Operon Technologies(Cologne,Germany), and then map them to the
> current version of the UniGene database.
>   How to run the procdure? Any advice and suggestions will be much
> appreciated.

There isn't necessarily a "procedure".  You could use the genbank accession
numbers from the three arrays as input to stanford Source to get a mapping
to recent unigene build.  You could also use the annotation packages from
Bioconductor to do the same thing, though I'm not sure what operon set you
are using and whether there is an annotation package available for it.  Once
you have each array mapped to a common identifier, you can use the functions
"match", "intersect", "union", and "%in%" to determine overlaps in the
different sets.


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