[BioC] RMA in Bioconductor versus APT - missing probesets

[Michal Blazejczyk]

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