[BioC] aroma.affymetrix and affy - different results

[Mark Robinson]

Markus.

The aroma.affymetrix processing is based on the defaults of affyPLM's  
'fitPLM', which is: background.method = "RMA.2" and normalize.method =  
"quantile".

Here is a test script that I wrote about a year ago (so take it with a  
grain of salt):
http://bioinf.wehi.edu.au/folders/mrobinson/for_hb/u133.test.mark.R

My test was based on the chip effects and they matched up, so  
presumably the BG adjustment and normalization also matched.  I  
believe a variation of this test is used everytime aroma.affymetrix is  
built.  Note I haven't used the 'extractAffyBatch' and I'm not sure if  
that introduces any differences in the order, etc.

Sorry, I haven't answered your question as I don't have access to run  
my code at the moment ... but hopefully this give you an avenue to  
check.

Mark


On 03/07/2008, at 10:49 PM, Markus Schmidberger wrote:

> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: 03 9345 2628
f: 03 9347 0852