GCRMA: error / warning
1
0
Entering edit mode
Guido Hooiveld ★ 3.9k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …
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]]
probe gcrma probe gcrma • 1.1k views
ADD COMMENT
0
Entering edit mode
Zhijin Wu ▴ 260
@zhijin-wu-2378
Last seen 9.6 years ago
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
ADD COMMENT

Login before adding your answer.

Traffic: 484 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6