[BioC] aroma.affymetrix and affy - different results
schmidi
schmidberger at gmx.at
Fri Jul 4 14:54:17 CEST 2008
Hi,
this was only a testcode, therefore I did quantile normalization at
the unadjusted signals.
Now I used
qn <- QuantileNormalization(cs, typesToUpdate="pm")
and still get a BIG DIFFERENCES:
all.equal(exprs(affyBatch_norm), exprs(affyBatch_aroma_norm))
[1] "Attributes: < Component 2: Component 2: 10 string mismatches >"
[2] "Mean relative difference: 0.2979911"
The differences in the background corrected sig
Best
Markus
On Jul 4, 2:16 pm, "Ken Simpson" <ken.m.simp... at gmail.com> wrote:
> Further to Mark's email, it is not the probe ordering that is the problem
> (note that the difference in the background corrected signals is ~ 1e-8),
> but the following line:
>
> > qn <- QuantileNormalization(cs, typesToAvg="pm")
>
> This is telling aroma.affymetrix to average the quantiles from the PM only
> to get the target distribution. However, by default, the normalisation will
> adjust *all* the signals using the target distribution, not just the PM -
> hence the difference Markus is seeing. If this line is changed to
>
> > qn <- QuantileNormalization(cs, typesToUpdate="pm")
>
> then you should see very little difference between the two implementations
> (~ 1e-5 in the test run I did). By default, typesToAvg = typesToUpdate and
> so this call will average the PM quantiles (typesToAvg="pm"), and update
> *only* the PM signals (typesToUpdate="pm").
>
> (Markus - I'm not sure why you performed background correction but then
> quantile normalised the unadjusted signals - was this just for testing
> purposes?)
>
> Cheers,
>
> Ken
>
> On Fri, Jul 4, 2008 at 10:07 AM, Mark Robinson <mrobin... at wehi.edu.au>
> wrote:
>
>
>
> > 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.deMail: Markus.Schmidberger
> > > [at] ibe.med.uni-muenchen.de
> > > Tel: +49 (089) 7095 - 4599
>
> > > _______________________________________________
> > > Bioconductor mailing list
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> > > Search the archives:
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>
> > ------------------------------
> > Mark Robinson
> > Epigenetics Laboratory, Garvan
> > Bioinformatics Division, WEHI
> > e: m.robin... at garvan.org.au
> > e: mrobin... at wehi.edu.au
> > p: 03 9345 2628
> > f: 03 9347 0852
> > ------------------------------
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