[BioC] RMA in Bioconductor versus APT - missing probesets

[cstrato]

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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