Hi, I have several affy drosophila v2 genome chip CEL files which I want to read-in using 'affy'. I get the following error with pure rma() and gcrma(). Also the use of expresso for conversion to an ExpressionSet fails. The basic call is: library(affy) library(gcrma) > r <- ReadAffy(celfile.path="fly_affy/CEL/") > r AffyBatch object size of arrays=732x732 features (17 kb) cdf=Drosophila_2 (18952 affyids) number of samples=20 number of genes=18952 annotation=drosophila2 notes= > eset_gcrma <- gcrma(r) Adjusting for optical effect....................Done. Computing affinities[1] Adjusting for non-specific binding....................Done. Normalizing Calculating Expression Fehler in rma(object, subset = subset, background = FALSE, normalize = normalize, : VECTOR_ELT() can only be applied to a 'list', not a 'character' Does somebody know why the conversion fails? Regards, Tobias > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu locale: LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C ;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;L C_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] drosophila2probe_2.3.0 gcrma_2.14.1 matchprobes_1.14.1 [4] drosophila2cdf_2.3.0 affy_1.20.2 Biobase_2.2.2 [7] limma_2.16.5 loaded via a namespace (and not attached): [1] affyio_1.10.1 preprocessCore_1.4.0

UPDATE / SOLVED: A variant of the problem has been described previously. I solved it by installing the current R-2.9.1 and bioconductor packages. The config ist now: > sessionInfo() R version 2.9.1 (2009-06-26) x86_64-unknown-linux-gnu locale: LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C ;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;L C_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] drosophila2probe_2.4.0 AnnotationDbi_1.6.1 drosophila2cdf_2.4.0 [4] gcrma_2.16.0 Biostrings_2.12.8 IRanges_1.2.3 [7] affy_1.22.0 Biobase_2.4.1 limma_2.18.2 loaded via a namespace (and not attached): [1] DBI_0.2-4 RSQLite_0.7-1 affyio_1.12.0 [4] preprocessCore_1.6.0 splines_2.9.1 tcltk_2.9.1 [7] tools_2.9.1 Tobias Petri schrieb: > Hi, > > I have several affy drosophila v2 genome chip CEL files which I want to > read-in using 'affy'. I get the following error with > pure rma() and gcrma(). Also the use of expresso for conversion to an > ExpressionSet fails. The basic call is: > > library(affy) > library(gcrma) > > >> r <- ReadAffy(celfile.path="fly_affy/CEL/") >> > > >> r >> > AffyBatch object > size of arrays=732x732 features (17 kb) > cdf=Drosophila_2 (18952 affyids) > number of samples=20 > number of genes=18952 > annotation=drosophila2 > notes= > > >> eset_gcrma <- gcrma(r) >> > Adjusting for optical effect....................Done. > Computing affinities[1] > Adjusting for non-specific binding....................Done. > Normalizing > Calculating Expression > Fehler in rma(object, subset = subset, background = FALSE, normalize = > normalize, : > VECTOR_ELT() can only be applied to a 'list', not a 'character' > > Does somebody know why the conversion fails? > > Regards, > Tobias > > >> sessionInfo() >> > R version 2.9.0 (2009-04-17) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY =C;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C ;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] drosophila2probe_2.3.0 gcrma_2.14.1 matchprobes_1.14.1 > [4] drosophila2cdf_2.3.0 affy_1.20.2 Biobase_2.2.2 > [7] limma_2.16.5 > > loaded via a namespace (and not attached): > [1] affyio_1.10.1 preprocessCore_1.4.0 > > _______________________________________________ > 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 > > -- =============================================================== Tobias Petri =============================================================== LFE Bioinformatik Amalienstr. 17 80333 M?nchen, DE =============================================================== mail : tobias.petri at bio.ifi.lmu.de phone : +49 89 2180 4042 web : http://www.bio.ifi.lmu.de/mitarbeiter/tobias-petri ===============================================================