Hi Sebastian.
2010/12/3 Sebastian Schönherr <ratsc...@gmail.com>:
> Hi there,
> I've a question regarding to RMA in aroma:
> In a first step we've compared the normalization method used in aroma
> with the method used in the Affymetrix Powertools which gave us
> identical results. (500K chip) ("QuantileNormalization(cs)" vs "apt-
> cel-transformer")
Thanks for this information. It is really useful. If you are not
aware of it already, we're collecting results of this kind at:
http://aroma-project.org/replication/
Would you mind writing down/sharing the details on exactly how you did
the comparison, e.g. one R/aroma script and one APT script? How do
you conclude they give identical results, e.g. by correlation,
graphical, ...?
> So in a next step we wanted to test median polish as well (standard
> flavor) on this data and compared it again to Affymetrix (using "apt-
> probeset-summarize" with med-polish,expr.genotype=true). We tried hard
> and tested a lot of configurations but we've never got the same
> results. (Same trend, but slightly different in the digits after the
> comma).
> R-script, quite straight forward:
> cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Nsp");
> cs <- AffymetrixCelSet$byName("testset", cdf=cdf);
> qn <- QuantileNormalization(cs);
> csN <- process(qn);
> plm <- RmaPlm(csN);
> fit(plm);
Atually, the default for the RmaPlm class is actually
flavor="affyPLM", which uses the robust linear model M-estimator as
implemented by preprocessCore/affyPLM. In
http://aroma-project.org/replication/RMA we show that aroma.affymetrix
can reproduce the affyPLM estimates quiet well. To use the median
polish estimator, use flavor="oligo". In
http://aroma-project.org/replication/gcRMA we use that to show that
aroma.affymetrix can reproduce gcrrma too. Likewise, justSNPRMA() for
AffymetrixCelSet uses flavor="oligo" to reproduce SNPRMA pipeline of
the oligo package, cf. http://aroma-project.org/replication/SNPRMA
Hope this helps
/Henrik
> The background correction was omitted in both scripts
> Any ideas?
> Thanks for your help
> Sebastian
>
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