[BioC] RMA in Bioconductor versus APT - missing probesets

[Michal Blazejczyk]

Dear Mark,

Thank you for your answer.

Please correct me if I'm getting the wrong impression, but doesn't this mean
that just.rma() and rma() are simply wrong in this case?  And if that's the case
then should they be used for ST data?  In previous versions of Biocionductor they
simply did not work (there was no cdf environment) but now that they do users will
be using them, generating results that are not complete...

Best,
Michał



Mark Cowley <m.cowley at garvan.org.au> wrote:
> 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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