[BioC] RMA in Bioconductor versus APT - missing probesets

[Michal Blazejczyk]

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
> _._._._._._._._._._._._._._._._._._
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> 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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