Hello, I get an error using "normalize.AffyBatch.vsn()" Simple Testcode and sessionInfo(): > data(affybatch.example) > a <- affybatch.example > normalize.AffyBatch.vsn(a) Fehler in validObject(.Object) : invalid class "vsnInput" object: 'subsample' must be a numeric vector of length 1 with values between 0 and 2400. > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETAR Y=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] vsn_3.6.0 limma_2.14.4 affy_1.18.1 preprocessCore_1.2.0 affyio_1.8.0 [6] Biobase_2.0.1 lattice_0.17-6 loaded via a namespace (and not attached): [1] grid_2.7.0 ################################################## I think the predefined subsample is to big ( subsample = 30000L -> subsample = 0L ) If I define a smaller subsample, then it works. But I get a wrong AffyBatch! > normalize.AffyBatch.vsn(a, subsample=1000) vsn: 2400 x 3 matrix (1 stratum). 0% done. 14% done. 28% done. 42% done. 57% done. 71% done. 85% done. 100% done. Please use 'meanSdPlot' to verify the fit. AffyBatch out-of-date; consider 'updateObject(<affybatch>)' AffyBatch object size of arrays=100x100 features (27 kb) cdf=cdfenv.example (150 affyids) number of samples=3 number of genes=150 annotation= notes= ###################################### If I use justvsn(), it works. But again, I will get a WRONG AffyBatch! > justvsn(a) vsn: 10000 x 3 matrix (1 stratum). 0% done. 25% done. 50% done. 75% done. 100% done. Please use 'meanSdPlot' to verify the fit. AffyBatch out-of-date; consider 'updateObject(<affybatch>)' AffyBatch object size of arrays=100x100 features (7 kb) cdf=cdfenv.example (150 affyids) number of samples=3 number of genes=150 annotation= notes= Do I have to think about this warning? Thanks Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r 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

Dear Markus, thank you for point this out! The first problem you reported is now fixed in vsn_3.7.4 (soon here: http://www.bioconductor.org/packages/2.3/bioc/html/vsn.html) This would have only affected very small AffyBatches (genechips with less than 30000 probes), but anyway the code now also deals properly with these. The second problem: normalize.AffyBatch.vsn and the justvsn and vsn2 methods for AffyBatch actually just make a copy of whatever object is given to them, modify the "exprs" slot, and return it. Hence the problem is with the "affybatch.example" dataset from the affy package. I cc its maintainer :) Try with, e.g. the "Dilution" data from the affydata package, all should be fine. Best wishes Wolfgang Markus Schmidberger a ?crit 10/06/2008 15:42: > Hello, > > I get an error using "normalize.AffyBatch.vsn()" > > Simple Testcode and sessionInfo(): > > > data(affybatch.example) > > a <- affybatch.example > > normalize.AffyBatch.vsn(a) > Fehler in validObject(.Object) : > invalid class "vsnInput" object: 'subsample' must be a numeric vector > of length 1 with values between 0 and 2400. > > sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > locale: > LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONET ARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets > methods base other attached packages: > [1] vsn_3.6.0 limma_2.14.4 affy_1.18.1 > preprocessCore_1.2.0 affyio_1.8.0 [6] Biobase_2.0.1 > lattice_0.17-6 loaded via a namespace (and not attached): > [1] grid_2.7.0 > > ################################################## > > I think the predefined subsample is to big ( subsample = 30000L -> > subsample = 0L ) > If I define a smaller subsample, then it works. But I get a wrong > AffyBatch! > > > normalize.AffyBatch.vsn(a, subsample=1000) > vsn: 2400 x 3 matrix (1 stratum). 0% done. > 14% done. > 28% done. > 42% done. > 57% done. > 71% done. > 85% done. > 100% done. > Please use 'meanSdPlot' to verify the fit. > AffyBatch out-of-date; consider 'updateObject(<affybatch>)' > AffyBatch object > size of arrays=100x100 features (27 kb) > cdf=cdfenv.example (150 affyids) > number of samples=3 > number of genes=150 > annotation= > notes= > > ###################################### > > If I use justvsn(), it works. But again, I will get a WRONG AffyBatch! > > > justvsn(a) > vsn: 10000 x 3 matrix (1 stratum). 0% done. > 25% done. > 50% done. > 75% done. > 100% done. > Please use 'meanSdPlot' to verify the fit. > AffyBatch out-of-date; consider 'updateObject(<affybatch>)' > AffyBatch object > size of arrays=100x100 features (7 kb) > cdf=cdfenv.example (150 affyids) > number of samples=3 > number of genes=150 > annotation= > notes= > Do I have to think about this warning? > > Thanks > Markus > -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber