[BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene

[Mikhail Pachkov]

Dear Henrik and Benilton,

Thank you for explanations. I have tried plotDensity with types="pm"
and results now look consistent.
I have also found that oligo::rma perform summarization to the
*probeset* level not probe level. I guess that is why my plots looked
so different. I have used rma.background.correct from preprocessCore
and now data look close to each other.

I would like to ask Henrik, how can I get probe id list within
aroma.affymetrix in order to print table of probe id and corresponding
expression values?

Kind regards,

Mikhail