[BioC] aroma.affymetrix and affy - different results

[Markus Schmidberger]

Hi,

I compared results from aroma.affymetrix and affy. Especially for rma 
background correction and quantil normalization. But there are DIFFERENCES!

Any ideas for these differences?
Attached my test code.

Best
Markus

########################################################
Code:

cs <- AffymetrixCelSet$fromName("test", chipType="HG-U133_Plus_2")
cs <- extract(cs, 1:10)
bc <- RmaBackgroundCorrection(cs)
csBC <- process(bc)
affyBatch_aroma_bgc <- extractAffyBatch(csBC)

qn <- QuantileNormalization(cs, typesToAvg="pm")
csN <- process(qn)
affyBatch_aroma_norm <- extractAffyBatch(csN)

pathCELFiles <- "/home/schmidb/tmp/rawData/test/HG-U133_Plus_2"
celFile <- list.celfiles(path=pathCELFiles,full.names=TRUE);
affyBatch <- ReadAffy(filenames=celFile[1:10])
affyBatch_bgc <- bg.correct(affyBatch, method="rma")
affyBatch_norm <- normalize.AffyBatch.quantiles(affyBatch, type="pmonly")

###########################################################
Comparison:

all.equal(exprs(affyBatch_bgc), exprs(affyBatch_aroma_bgc))
    [1] "Attributes: < Component 2: Component 2: 10 string mismatches >"
    [2] "Mean relative difference: 2.300415e-08" 

all.equal(exprs(affyBatch_norm), exprs(affyBatch_aroma_norm))
[1] "Attributes: < Component 2: Component 2: 10 string mismatches >"
[2] "Mean relative difference: 0.2979911"

(sampleNames are the same!)

####################################################
sessionInfo()
R version 2.7.1 (2008-06-23)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY=C;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods 
[8] base    

other attached packages:
 [1] hgu133plus2cdf_2.2.0   affyPara_1.1.5         snow_0.3-0           
 [4] aroma.affymetrix_0.9.3 aroma.apd_0.1.3        R.huge_0.1.5         
 [7] affxparser_1.12.2      aroma.core_0.9.3       sfit_0.1.5           
[10] aroma.light_1.8.1      digest_0.3.1           matrixStats_0.1.2    
[13] R.rsp_0.3.4            R.cache_0.1.7          R.utils_1.0.2        
[16] R.oo_1.4.3             R.methodsS3_1.0.1      affy_1.18.2          
[19] preprocessCore_1.2.0   affyio_1.8.0           Biobase_2.0.1        

-- 
Dipl.-Tech. Math. Markus Schmidberger

Ludwig-Maximilians-Universität München
IBE - Institut für medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
URL: http://ibe.web.med.uni-muenchen.de 
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
Tel: +49 (089) 7095 - 4599