Hello, I think there may be a problem with the current version of arrayQualityMetrics. I have downloaded two CEL files from GEO, read them into an AffyBatch object using the function ReadAffy. The object looks good to me. > AB.Endoh AffyBatch object size of arrays=1002x1002 features (17 kb) cdf=Mouse430_2 (45101 affyids) number of samples=2 number of genes=45101 annotation=mouse4302 When I now call arrayQualityMetrics on this object, no result files are produced and I receive the following errors: > arrayQualityMetrics(AB.Endoh, outdir="aqm_raw", do.logtransform=TRUE) The directory 'aqm_raw' has been created. Error in `sampleNames<-`(`*tmp*`, value = NULL) : number of new names (0) should equal number of rows in AnnotatedDataFrame (2) Error in obj[[i]]$legend : $ operator is invalid for atomic vectors In addition: Warning message: In arrayQualityMetrics(AB.Endoh, outdir = "aqm_raw", do.logtransform = TRUE) : Cannot draw the RNA degradation plot However, creating the RNA degradation plot and other plots by hand works well. For example, > D <- AffyRNAdeg(AB.Endoh) > plotAffyRNAdeg(D) gives the correct plot. So it looks like there is a problem with arrayQualityMetrics. My sessionInfo output is: > sessionInfo() R version 2.11.0 Under development (unstable) (2009-10-27 r50222) x86_64-unknown-linux-gnu attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] mouse4302cdf_2.5.0 org.Mm.eg.db_2.3.6 [3] RSQLite_0.7-3 DBI_0.2-4 [5] AnnotationDbi_1.9.2 biomaRt_2.3.0 [7] arrayQualityMetrics_2.5.2 affyPLM_1.23.0 [9] preprocessCore_1.9.0 gcrma_2.19.0 [11] mouse4302mmentrezgcdf_12.0.0 vsn_3.15.0 [13] affy_1.25.2 Biobase_2.7.0 loaded via a namespace (and not attached): [1] affyio_1.15.1 annotate_1.25.0 beadarray_1.15.0 Biostrings_2.15.6 [5] genefilter_1.29.2 grid_2.11.0 hwriter_1.1 IRanges_1.5.6 [9] lattice_0.17-26 latticeExtra_0.6-4 limma_3.3.1 marray_1.25.0 [13] RColorBrewer_1.0-2 RCurl_1.3-0 simpleaffy_2.23.0 splines_2.11.0 [17] stats4_2.11.0 survival_2.35-7 tools_2.11.0 XML_2.6-0 [21] xtable_1.5-6 --- Joern Toedling Institut Curie -- U900 26 rue d'Ulm, 75005 Paris, FRANCE Tel. +33 (0)156246927

Hi Joern, Thank you for your feedback. You are using the development version 2.5.2 and I have recently added legend on the RNA Degradation plot of this version, apparently I need to correct it. The release version 2.4.2 should not have this problem. Best wishes, Audrey > Hello, > > I think there may be a problem with the current version of > arrayQualityMetrics. I have downloaded two CEL files from GEO, read them > into > an AffyBatch object using the function ReadAffy. The object looks good to > me. > >> AB.Endoh > AffyBatch object > size of arrays=1002x1002 features (17 kb) > cdf=Mouse430_2 (45101 affyids) > number of samples=2 > number of genes=45101 > annotation=mouse4302 > > When I now call arrayQualityMetrics on this object, no result files are > produced and I receive the following errors: > >> arrayQualityMetrics(AB.Endoh, outdir="aqm_raw", do.logtransform=TRUE) > The directory 'aqm_raw' has been created. > Error in `sampleNames<-`(`*tmp*`, value = NULL) : > number of new names (0) should equal number of rows in > AnnotatedDataFrame (2) > Error in obj[[i]]$legend : $ operator is invalid for atomic vectors > In addition: Warning message: > In arrayQualityMetrics(AB.Endoh, outdir = "aqm_raw", do.logtransform = > TRUE) : > Cannot draw the RNA degradation plot > > However, creating the RNA degradation plot and other plots by hand works > well. > For example, > >> D <- AffyRNAdeg(AB.Endoh) >> plotAffyRNAdeg(D) > > gives the correct plot. > > So it looks like there is a problem with arrayQualityMetrics. > > My sessionInfo output is: > >> sessionInfo() > R version 2.11.0 Under development (unstable) (2009-10-27 r50222) > x86_64-unknown-linux-gnu > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] mouse4302cdf_2.5.0 org.Mm.eg.db_2.3.6 > [3] RSQLite_0.7-3 DBI_0.2-4 > [5] AnnotationDbi_1.9.2 biomaRt_2.3.0 > [7] arrayQualityMetrics_2.5.2 affyPLM_1.23.0 > [9] preprocessCore_1.9.0 gcrma_2.19.0 > [11] mouse4302mmentrezgcdf_12.0.0 vsn_3.15.0 > [13] affy_1.25.2 Biobase_2.7.0 > > loaded via a namespace (and not attached): > [1] affyio_1.15.1 annotate_1.25.0 beadarray_1.15.0 > Biostrings_2.15.6 > [5] genefilter_1.29.2 grid_2.11.0 hwriter_1.1 > IRanges_1.5.6 > [9] lattice_0.17-26 latticeExtra_0.6-4 limma_3.3.1 > marray_1.25.0 > [13] RColorBrewer_1.0-2 RCurl_1.3-0 simpleaffy_2.23.0 > splines_2.11.0 > [17] stats4_2.11.0 survival_2.35-7 tools_2.11.0 XML_2.6-0 > [21] xtable_1.5-6 > > > --- > Joern Toedling > Institut Curie -- U900 > 26 rue d'Ulm, 75005 Paris, FRANCE > Tel. +33 (0)156246927 > > _______________________________________________ > 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 >