Problems with RMA in affy
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anupam sinha ▴ 270
@anupam-sinha-3207
Last seen 8.2 years ago
Dear all, I am trying to analyse a set of CEL files. But I am getting an error. Can anyone help me out with this? Thanks in advance. *> data<-ReadAffy() > data AffyBatch object size of arrays=1164x1164 features (10 kb) cdf=HG-U133_Plus_2 (54675 affyids) number of samples=12 number of genes=54675 annotation=hgu133plus2 notes= > eset<-rma(data) Background correcting Normalizing Error in rma(data) : VECTOR_ELT() can only be applied to a 'list', not a 'character' * *> sessionInfo() R version 2.9.0 (2009-04-17) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] cMAP_1.15.1 yeastExpData_0.9.9 graph_1.20.0 [4] hgu133plus2cdf_2.4.0 affy_1.16.0 preprocessCore_1.6.0 [7] affyio_1.6.1 Biobase_2.4.0 loaded via a namespace (and not attached): [1] cluster_1.11.13 tools_2.9.0 *Regards, Anupam [[alternative HTML version deleted]]
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@martin-morgan-1513
Last seen 7 days ago
United States
Hi Anupam -- Your packages are out of date. Follow the instructions at http://bioconductor.org/docs/install/ to update. Martin anupam sinha <anupam.contact at="" gmail.com=""> writes: > Dear all, > I am trying to analyse a set of CEL files. But I am getting an > error. Can anyone help me out with this? Thanks in advance. > > > > *> data<-ReadAffy() >> data > AffyBatch object > size of arrays=1164x1164 features (10 kb) > cdf=HG-U133_Plus_2 (54675 affyids) > number of samples=12 > number of genes=54675 > annotation=hgu133plus2 > notes= >> eset<-rma(data) > Background correcting > Normalizing > Error in rma(data) : > VECTOR_ELT() can only be applied to a 'list', not a 'character' > * > *> sessionInfo() > R version 2.9.0 (2009-04-17) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] cMAP_1.15.1 yeastExpData_0.9.9 graph_1.20.0 > [4] hgu133plus2cdf_2.4.0 affy_1.16.0 preprocessCore_1.6.0 > [7] affyio_1.6.1 Biobase_2.4.0 > > loaded via a namespace (and not attached): > [1] cluster_1.11.13 tools_2.9.0 > > > *Regards, > > Anupam > > [[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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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@james-w-macdonald-5106
Last seen 7 hours ago
United States
Hi Anupam, anupam sinha wrote: > Dear all, > I am trying to analyse a set of CEL files. But I am getting an > error. Can anyone help me out with this? Thanks in advance. Sure, just update your packages the correct way. You somehow have a mixture of really old affy and affyio packages with a nearly current Biobase, which would never happen if you had installed your bioconductor packages using biocLite(). The easiest for you would be to start a new R session, then source("http://www.bioconductor.org/biocLite.R") biocLite("Biobase") library(Biobase) z <- biocReposList() update.packages(repos = z, ask = FALSE) Best, Jim > > > > *> data<-ReadAffy() >> data > AffyBatch object > size of arrays=1164x1164 features (10 kb) > cdf=HG-U133_Plus_2 (54675 affyids) > number of samples=12 > number of genes=54675 > annotation=hgu133plus2 > notes= >> eset<-rma(data) > Background correcting > Normalizing > Error in rma(data) : > VECTOR_ELT() can only be applied to a 'list', not a 'character' > * > *> sessionInfo() > R version 2.9.0 (2009-04-17) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] cMAP_1.15.1 yeastExpData_0.9.9 graph_1.20.0 > [4] hgu133plus2cdf_2.4.0 affy_1.16.0 preprocessCore_1.6.0 > [7] affyio_1.6.1 Biobase_2.4.0 > > loaded via a namespace (and not attached): > [1] cluster_1.11.13 tools_2.9.0 > > > *Regards, > > Anupam > > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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Thanks a million fro all your suggestions. I will implement them. Regards, Anupam [[alternative HTML version deleted]]
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