[BioC] select one Affy probeset for one gene

[Glazko, Galina]

Dear Sean,

Thank you for the answer.
This sounds good but what if I do multiple testing?
Then my adjusted p-values are based on the entire array, and I will not
be able to see differentially expressed genes because I am testing say
40,000 hypotheses, while there are actually as many hypotheses as there
are genes.
I would appreciate if you could give me some references to the papers
where this question was discussed.

Best regards
Galina

-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
Sent: Monday, March 13, 2006 4:05 PM
To: Glazko, Galina; Bioconductor
Subject: Re: [BioC] select one Affy probeset for one gene




On 3/13/06 3:38 PM, "Glazko, Galina" <Galina_Glazko at urmc.rochester.edu>
wrote:

> Dear list,
> 
>  
> 
> Is there a way to automatically select one probeset for one gene in
Affy
> arrays? 
> 
> Say, if we have several probesets for a given gene, we select the one
> with the highest level of expression, or based on any other reasonable
> criteria...?
> 
> I am sorry if this question was answered before, it seems to be very
> basic question and I hope there is the solution...

Galina,

You can contrive a solution, I suppose.  However, I'm not sure this is a
good idea.  Whatever "reasonable criteria" you use are likely to lead to
bias.  Filtering on unmeasured probesets or other quality measures
applied
equally to all probesets is probably reasonable, but not applying on a
per-gene basis.  There have been related discussions in the past, often
centering around "averaging" expression values.

The more accepted way of dealing with multiple probesets is to do your
analysis based on the probeset; only after that is done do you then
connect
your gene labels back to the probesets.

Sean