[BioC] how deal with multiplicate affy probes?

[Michael Seewald]

As a rule of thumb: If statistics based on a given probe set data tells you,
that a transcript is significantly deregulated, you can usually trust it and
discard every other probe set for that transcript!

The thing to look at is the probe design itself: Download the probe set from
NetAffx and blast the single probes agains the genome (e.g. in ensembl). You
will be surprised, how many probes match up with introns or genomic regions
that do not correspond to any cDNA!

2 examples: There are 4 probe sets for human Wnt6 (HG-U133AB), 2 match with
the sense (!) strand and have to be discarded. Out of >12 probe sets for human
CD44, only 4 have probes that are completely matching the transcripts. >8 can
be discarded.

Best,
Michael

PS: www.ensembl.org is always a good place to check probe sets. Their mapping
of probe sets does not show the location of single probes, though...

PPS: In affymetrix.com you can check out the "Details" view for a probe set.
There you can discover, that 2 probe sets of Wnt 6 map to the (-) strand,
which is bad. It doesn't tell you, however, that many probe sets match intron
regions.


On Sat, 20 Mar 2004, Johnnidis, Jonathan wrote:
> I'm a new list member and am not quite sure if this question is appropriate
> for the list, but will shoot anyway. I'm analyzing a bunch of data from Affy
> MgU74Av2 chips and am a bit perplexed as to how to treat conflicting
> expression data from multiplicate probe sets (that is a gene that has >1
> probe set designed against it (for example, 97569_r_at and 97658_r_at are
> both probes for the Insulin gene).