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

[Benilton Carvalho]

Dear Mikhail,

when you read the CEL files, you have the information at the probe
level. So, when you summarize, you will summarize to a 'less granular'
level (in this case probeset).

Maybe what you're trying to achieve is the comparison of the
background correction (or possibly normalization) method *before*
summarization?

b

On Fri, Feb 26, 2010 at 4:38 PM, Mikhail Pachkov <pachkov at gmail.com> wrote:
> 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
>
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