[BioC] how deal with multiplicate affy probes?

[Lawrence Paul Petalidis]

Hello,
As a note following on from Michael Seewald's message, I totally agree that
there is a STRONG need to BLAST probe set sequences. I tend to use the probe
set target sequence instead of the indicidual probe sequences however. You
will be surprised to see the inconsistency of the Affy annotation, in many
cases _at probes are really not unique at all. So if you are really
interested in a transcript, BLAST it to make sure you are actually seeing
what you think you are.

Best regards to all, Lawrence

______________________________
Lawrence Paul Petalidis
Ph.D. Candidate

University of Cambridge
Department of Pathology
______________________________

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Michael
Seewald
Sent: 25 March 2004 20:48
To: Johnnidis, Jonathan
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] how deal with multiplicate affy probes?



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).

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