Dear List, I got error as follows when normolizing a AffyBatch Object (400 samples) with R 2.9.0. It works on an old version of R, R 2.6.1, on another computer but the computer can not handle so many samples due to memory issue. There is no problem to read in the cel files from both versions of R. Error in rma(dat) : VECTOR_ELT() can only be applied to a 'list', not a 'character' #dat is the AffyBatch Object #session info is as follows (got the above error): > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-redhat-linux-gnu attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] hgu133acdf_2.2.0 annaffy_1.12.1 KEGG.db_2.2.0 [4] GO.db_2.2.0 RSQLite_0.6-8 DBI_0.2-4 [7] AnnotationDbi_1.4.3 gplots_2.6.0 gdata_2.4.2 [10] gtools_2.5.0 MASS_7.2-46 RColorBrewer_1.0-2 [13] affyPLM_1.16.0 simpleaffy_2.16.0 gcrma_2.12.1 [16] matchprobes_1.12.0 genefilter_1.20.0 survival_2.35-4 [19] affy_1.18.1 preprocessCore_1.2.0 affyio_1.8.0 [22] marray_1.18.0 limma_2.14.4 Biobase_2.2.2 loaded via a namespace (and not attached): [1] annotate_1.18.0 #session info is as follows (no error, an older version R): > sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133plus2cdf_2.0.0 annaffy_1.10.0 KEGG_2.0.0 GO_2.0.0 [5] gplots_2.3.2 gdata_2.3.1 gtools_2.4.0 MASS_7.2-38 [9] RColorBrewer_1.0-1 affyPLM_1.14.0 simpleaffy_2.14.02 gcrma_2.10.0 [13] matchprobes_1.10.0 genefilter_1.16.0 survival_2.34 affy_1.16.0 [17] preprocessCore_1.0.0 affyio_1.6.0 marray_1.16.0 limma_2.12.0 [21] Biobase_1.16.0 It would be great if someone could help figure out what caused the error. Thank you! Fuying Gao

Hi Fuying, Your version of affy is not matching your version of R/Bioconductor. Please install/reinstall/update your packages following our instructions here: http://bioconductor.org/docs/install/ Failing to do so will give you no end of troubles... Cheers, H. Fuying Gao wrote: > Dear List, > > I got error as follows when normolizing a AffyBatch Object (400 samples) > with R 2.9.0. It works on an old version of R, R 2.6.1, on another > computer but the computer can not handle so many samples due to memory > issue. > There is no problem to read in the cel files from both versions of R. > > > Error in rma(dat) : > VECTOR_ELT() can only be applied to a 'list', not a 'character' > > #dat is the AffyBatch Object > > #session info is as follows (got the above error): > >> sessionInfo() > > R version 2.9.0 (2009-04-17) > x86_64-redhat-linux-gnu > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] hgu133acdf_2.2.0 annaffy_1.12.1 KEGG.db_2.2.0 > [4] GO.db_2.2.0 RSQLite_0.6-8 DBI_0.2-4 > [7] AnnotationDbi_1.4.3 gplots_2.6.0 gdata_2.4.2 > [10] gtools_2.5.0 MASS_7.2-46 RColorBrewer_1.0-2 > [13] affyPLM_1.16.0 simpleaffy_2.16.0 gcrma_2.12.1 > [16] matchprobes_1.12.0 genefilter_1.20.0 survival_2.35-4 > [19] affy_1.18.1 preprocessCore_1.2.0 affyio_1.8.0 > [22] marray_1.18.0 limma_2.14.4 Biobase_2.2.2 > > loaded via a namespace (and not attached): > [1] annotate_1.18.0 > > > > > > #session info is as follows (no error, an older version R): > >> sessionInfo() > > R version 2.6.1 (2007-11-26) > i386-pc-mingw32 > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] hgu133plus2cdf_2.0.0 annaffy_1.10.0 KEGG_2.0.0 > GO_2.0.0 > [5] gplots_2.3.2 gdata_2.3.1 gtools_2.4.0 > MASS_7.2-38 > [9] RColorBrewer_1.0-1 affyPLM_1.14.0 simpleaffy_2.14.02 > gcrma_2.10.0 > [13] matchprobes_1.10.0 genefilter_1.16.0 survival_2.34 > affy_1.16.0 > [17] preprocessCore_1.0.0 affyio_1.6.0 marray_1.16.0 > limma_2.12.0 > [21] Biobase_1.16.0 > > > It would be great if someone could help figure out what caused the error. > Thank you! > > Fuying Gao > > _______________________________________________ > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319