[BioC] RMA in Bioconductor versus APT - missing probesets

[Mark Cowley]

Michal,
in just.rma and rma, it was assumed that each probe could be in at most 1 probeset. once a probe was used, it cannot be reused. 
on the ST arrays, some probes can be in many probesets... so if you use rma, eventually, all the probes in a probeset have been used once by the time the current probeset needs it & you get NA's.

Mark

On 24/02/2011, at 8:40 AM, Michal Blazejczyk wrote:

> Dear Christian,
> 
> I am aware of the existence of xps.  However, we can't use it for our purposes,
> largely because it is too complicated to set up (or at least, that was the case
> the last time we looked at it).  I would still like to know what's happening in
> just.rma()  :)
> 
> Best,
> Michał
> 
> 
> 
> cstrato <cstrato at aon.at> wrote:
>> Dear Michal,
> 
>> As an alternative to just.rma() you could use the Bioconductor package 
>> xps which uses the Affymetrix PGF-file as well as the Affymetrix 
>> annotations, and thus should contain all probesets. xps has also a 
>> vignette, "APTvsXPS.pdf" which compares the results for RMA obtained 
>> from APT vs xps, respectively, for the HuGene 1.0 ST array.
> 
>> Best regards
>> Christian
>> _._._._._._._._._._._._._._._._._._
>> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
>> V.i.e.n.n.a           A.u.s.t.r.i.a
>> e.m.a.i.l:        cstrato at aon.at
>> _._._._._._._._._._._._._._._._._._
> 
> 
>> On 2/23/11 7:06 PM, Michal Blazejczyk wrote:
>>> Dear group,
>>> 
>>> I have noticed that Bioconductor's just.rma() function returns fewer transcript-level
>>> probesets that RMA in APT for the Human Gene 1.0 ST array.  To be specific, 819 probesets
>>> are missing, and most of them seem to be "real", i.e. they are annotated when I run them
>>> through NetAffx.
>>> 
>>> I would like to know why this is happening, and whether it is to be expected or maybe
>>> it is a bug.
>>> 
>>> Best regards,
>>> 
>>> Michał Błażejczyk
>>> FlexArray Lead Developer
>>> McGill University and Genome Quebec Innovation Centre
>>> http://www.gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=e
>>> 
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> 
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