Dear list, When executing GCRMA I encounter a problem. I would appreciate if some could point out what may be the cause of the error/warning [In Yin[subset] = y0.adj : number of items to replace is not a multiple of replacement length.] Thanks, Guido > library(affy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > library(limma) > library(gcrma) > > targets <- readTargets("targets_A48.txt") > data <- ReadAffy(filenames=targets$FileName, cdfname="Mouse4302_Mm_ENTREZG") > data AffyBatch object size of arrays=1002x1002 features (8 kb) cdf=Mouse4302_Mm_ENTREZG (16395 affyids) number of samples=9 number of genes=16395 annotation=mouse4302mmentrezg notes= > data.norm <- gcrma(data, fast=FALSE, affinity.source=c("local")) Adjusting for optical effect.........Done. Computing base-position profiles for probe affinitiesDone. Computing affinities.........Done. Adjusting for non-specific binding.........Done. Normalizing Calculating Expression Warning messages: 1: In Yin[subset] = y0.adj : number of items to replace is not a multiple of replacement length 2: In Yin[subset] = y0.adj : number of items to replace is not a multiple of replacement length 3: In Yin[subset] = y0.adj : number of items to replace is not a multiple of replacement length 4: In Yin[subset] = y0.adj : number of items to replace is not a multiple of replacement length 5: In Yin[subset] = y0.adj : number of items to replace is not a multiple of replacement length 6: In Yin[subset] = y0.adj : number of items to replace is not a multiple of replacement length 7: In Yin[subset] = y0.adj : number of items to replace is not a multiple of replacement length 8: In Yin[subset] = y0.adj : number of items to replace is not a multiple of replacement length 9: In Yin[subset] = y0.adj : number of items to replace is not a multiple of replacement length > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] mouse4302mmentrezgprobe_11.0.1 mouse4302mmentrezgcdf_11.0.1 gcrma_2.14.1 [4] matchprobes_1.14.0 limma_2.16.2 affy_1.20.0 [7] Biobase_2.2.0 loaded via a namespace (and not attached): [1] affyio_1.10.0 preprocessCore_1.4.0 ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> email: guido.hooiveld@wur.nl [[alternative HTML version deleted]]

Thank you for bringing up the problem. The bug is fixed in the devel version now. best, Jean Hooiveld, Guido wrote: > > Dear list, > When executing GCRMA I encounter a problem. I would appreciate if some > could point out what may be the cause of the error/warning [In > Yin[subset] = y0.adj : number of items to replace is not a multiple of > replacement length.] > > Thanks, > Guido > > >> library(affy) > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > >> library(limma) >> library(gcrma) >> >> targets <- readTargets("targets_A48.txt") > >> data <- ReadAffy(filenames=targets$FileName, > cdfname="Mouse4302_Mm_ENTREZG") >> data > AffyBatch object > size of arrays=1002x1002 features (8 kb) > cdf=Mouse4302_Mm_ENTREZG (16395 affyids) > number of samples=9 > number of genes=16395 > annotation=mouse4302mmentrezg > notes= > >> data.norm <- gcrma(data, fast=FALSE, affinity.source=c("local")) > Adjusting for optical effect.........Done. > Computing base-position profiles for probe affinitiesDone. > Computing affinities.........Done. > Adjusting for non-specific binding.........Done. > Normalizing > Calculating Expression > Warning messages: > 1: In Yin[subset] = y0.adj : > number of items to replace is not a multiple of replacement length > 2: In Yin[subset] = y0.adj : > number of items to replace is not a multiple of replacement length > 3: In Yin[subset] = y0.adj : > number of items to replace is not a multiple of replacement length > 4: In Yin[subset] = y0.adj : > number of items to replace is not a multiple of replacement length > 5: In Yin[subset] = y0.adj : > number of items to replace is not a multiple of replacement length > 6: In Yin[subset] = y0.adj : > number of items to replace is not a multiple of replacement length > 7: In Yin[subset] = y0.adj : > number of items to replace is not a multiple of replacement length > 8: In Yin[subset] = y0.adj : > number of items to replace is not a multiple of replacement length > 9: In Yin[subset] = y0.adj : > number of items to replace is not a multiple of replacement length > > >> sessionInfo() > R version 2.8.0 (2008-10-20) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] mouse4302mmentrezgprobe_11.0.1 mouse4302mmentrezgcdf_11.0.1 > gcrma_2.14.1 > [4] matchprobes_1.14.0 limma_2.16.2 > affy_1.20.0 > [7] Biobase_2.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.10.0 preprocessCore_1.4.0 > > > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > email: guido.hooiveld at wur.nl > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- ------------------------------------ Zhijin (Jean) Wu Assistant Professor of Biostatistics Brown University, Box G-S121 Providence, RI 02912 Tel: 401 863 1230 Fax: 401 863 9182 http://www.stat.brown.edu/zwu