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")
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);
The background correction was omitted in both scripts
Any ideas?
Thanks for your help
Sebastian
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