[BioC] RMA in Bioconductor versus APT - missing probesets

[Hooiveld, Guido]

Hi,
I think this is to be expected. I assume [since you did not included your sessionInfo()] you used the CDF environment that has been made form the *unsupported* CDF file Affymetrix provides. This unsupported CDF was generated by Affymetrix back in early 2007, and since then the annotation hence probeset definitions have been updated  (hg18 vs hg19), which may explain part of your observation. Also, at a certain moment Affymetrix decided to remove (ignore) probesets consisting of less than 4 probes.
See e.g. this post:
http://article.gmane.org/gmane.science.biology.informatics.conductor/20999
that mentions this for the mouse Gene ST array.

HTH,
Guido

------------------------------------------------ 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
email:      guido.hooiveld at wur.nl
internet:   http://nutrigene.4t.com 
http://www.researcherid.com/rid/F-4912-2010



-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Michal Blazejczyk
Sent: Wednesday, February 23, 2011 19:07
To: bioconductor at r-project.org
Subject: [BioC] RMA in Bioconductor versus APT - missing probesets

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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