[BioC] how deal with multiplicate affy probes?

[Michael Seewald]

On Tue, 30 Mar 2004, Sean Davis wrote:
> In reading my statement out of context, I should clarify a bit.  The problem
> is that the space in which one is searching for blast or blat "hits" is
> larger (unnecessarily large) in the genomic case as compared to the
> transcript case.

OK, now I see what you mean - and I disagree. ;)

I am not so much concerned about probes hitting multiple spots in the genome
(you can work that out) as rather probes hitting introns as opposed to 3'UTR
regions. As far as introns are concerned, you are right. The transcript
databases are good enough to tell us, this probe hits an intron or an exon.
However, I can remember a couple of cases, where I saw a probe hitting an UTR
region - and it gave excellent signal - and at the same time it did *NOT* map
to the transcript. In your analysis, you would miss that probe set. My
personal conclusion was, that a) the probe was ok and b) some transcript
sequences are 3'-truncated. I didn't dive into literature to check for
reasons, though. Of course, at some point, there must have been a transcript
displaying that very probe sequence, otherwise Affy wouldn't have taken it for
the design.

There are many more reasons to map everything to the genome - SNP analysis,
epigenetics, CGH are only some of them.

Best wishes,
Michael