Dear all, I am analyzing data obtained using the HuGene2.0-st arrays from affymetrix. I have used aroma for preprocessing and limma for diff. expression analysis. After multiple testing I lost significance and therefore I want to filter out genes that do not have a potential to be significantly different. So I have created an expression set after rma plm <- RmaPlm(csN) fit(plm, verbose=verbose) ces <- getChipEffectSet(plm) eset <- extractExpressionSet(ces) ans <- nsFilter(eset) I am getting an error at this point: Error in if (nchar(annChip) == 0) stop("'eset' must have a valid annotation slot") : argument is of length zero . I understand that is because the annotation field is empty. But how can I overcome this? Thanks Andreia the ces object ChipEffectSet: Name: Jurkat_0_vs_over_2 Tags: RBC,QN,RMA Path: Documents/analysis_affy_arrays/plmData/Jurkat_0_vs_over_2,RBC,QN,RMA /HuGene-2_0-st Platform: Affymetrix Chip type: HuGene-2_0-st,r3_binary,monocell Number of arrays: 6 Names: Ju_0_1_1, Ju_0_2_2, Ju_0_3_3, ..., Ju_34c_5_6 [6] Time period: 2013-03-27 16:56:07 -- 2013-03-27 16:56:08 Total file size: 3.08MB RAM: 0.01MB Parameters: {} the eset object: ExpressionSet (storageMode: lockedEnvironment) assayData: 53617 features, 6 samples element names: exprs protocolData: none phenoData: none featureData: none experimentData: use 'experimentData(object)' Annotation: sessionInfo() R version 2.15.3 (2013-03-01) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] C attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] hgu95av2.db_2.8.0 org.Hs.eg.db_2.8.0 RSQLite_0.11.2 DBI_0.2-5 AnnotationDbi_1.20.7 BiocInstaller_1.8.3 genefilter_1.40.0 [8] GenomeGraphs_1.18.0 biomaRt_2.14.0 limma_3.14.4 gplots_2.11.0 MASS_7.3-23 KernSmooth_2.23-10 caTools_1.14 [15] gdata_2.12.0 gtools_2.7.1 Biobase_2.18.0 BiocGenerics_0.4.0 aroma.affymetrix_2.8.0 affxparser_1.30.2 aroma.apd_0.2.3 [22] R.huge_0.4.1 aroma.light_1.28.0 aroma.core_2.8.3 matrixStats_0.6.2 R.rsp_0.8.2 R.devices_2.1.3 R.cache_0.6.5 [29] R.filesets_2.0.0 R.utils_1.23.2 R.oo_1.13.0 affy_1.36.1 R.methodsS3_1.4.2 loaded via a namespace (and not attached): [1] IRanges_1.16.6 PSCBS_0.30.0 RCurl_1.95-4.1 XML_3.96-1.1 affyio_1.26.0 annotate_1.36.0 bitops_1.0-4.2 [8] digest_0.6.3 parallel_2.15.3 preprocessCore_1.20.0 splines_2.15.3 stats4_2.15.3 survival_2.37-4 tools_2.15.3 [15] xtable_1.7-1 zlibbioc_1.4.0 ---------------------------------------------------------------------- ----------------------- Andreia J. Amaral, PhD BioFIG - Center for Biodiversity, Functional and Integrative Genomics Instituto de Medicina Molecular University of Lisbon Tel: +352 217500000 (ext. office: 28253) email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt [[alternative HTML version deleted]]

Dear Andreia do you need the 'nsFilter' filter function for this purpose (which is great but perhaps a bit over-engineered) or would you already be helped by doing this using basic R functionality, e.g. m = rowMeans(exprs(eset)) esetf = eset[ m> quantile(m, probs=theta), ] Please also note the new vignette on filtering, http://www.bioconductor.org/packages/devel/bioc/html/genefilter.html --> Diagnostics for independent filtering. Hope this helps Wolfgang El Apr 1, 2013, a las 4:32 pm, Andreia Fonseca <andreia.fonseca at="" gmail.com=""> escribi?: > Dear all, > > > I am analyzing data obtained using the HuGene2.0-st arrays from affymetrix. > > I have used aroma for preprocessing and limma for diff. expression > analysis. After multiple testing I lost significance and therefore I want > to filter out genes that do not have a potential to be significantly > different. > > So I have created an expression set after rma > > > plm <- RmaPlm(csN) > > fit(plm, verbose=verbose) > > ces <- getChipEffectSet(plm) > > eset <- extractExpressionSet(ces) > > ans <- nsFilter(eset) > > I am getting an error at this point: > > Error in if (nchar(annChip) == 0) stop("'eset' must have a valid annotation > slot") : > argument is of length zero > > . > > I understand that is because the annotation field is empty. But how can I > overcome this? > > Thanks Andreia > > the ces object > > ChipEffectSet: > Name: Jurkat_0_vs_over_2 > Tags: RBC,QN,RMA > Path: > Documents/analysis_affy_arrays/plmData/Jurkat_0_vs_over_2,RBC,QN,RMA /HuGene-2_0-st > Platform: Affymetrix > Chip type: HuGene-2_0-st,r3_binary,monocell > Number of arrays: 6 > Names: Ju_0_1_1, Ju_0_2_2, Ju_0_3_3, ..., Ju_34c_5_6 [6] > Time period: 2013-03-27 16:56:07 -- 2013-03-27 16:56:08 > Total file size: 3.08MB > RAM: 0.01MB > Parameters: {} > > the eset object: > > ExpressionSet (storageMode: lockedEnvironment) > assayData: 53617 features, 6 samples > element names: exprs > protocolData: none > phenoData: none > featureData: none > experimentData: use 'experimentData(object)' > Annotation: > > > sessionInfo() > > R version 2.15.3 (2013-03-01) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] hgu95av2.db_2.8.0 org.Hs.eg.db_2.8.0 RSQLite_0.11.2 > DBI_0.2-5 AnnotationDbi_1.20.7 BiocInstaller_1.8.3 > genefilter_1.40.0 > [8] GenomeGraphs_1.18.0 biomaRt_2.14.0 limma_3.14.4 > gplots_2.11.0 MASS_7.3-23 KernSmooth_2.23-10 > caTools_1.14 > [15] gdata_2.12.0 gtools_2.7.1 Biobase_2.18.0 > BiocGenerics_0.4.0 aroma.affymetrix_2.8.0 affxparser_1.30.2 > aroma.apd_0.2.3 > [22] R.huge_0.4.1 aroma.light_1.28.0 aroma.core_2.8.3 > matrixStats_0.6.2 R.rsp_0.8.2 R.devices_2.1.3 > R.cache_0.6.5 > [29] R.filesets_2.0.0 R.utils_1.23.2 R.oo_1.13.0 > affy_1.36.1 R.methodsS3_1.4.2 > > loaded via a namespace (and not attached): > [1] IRanges_1.16.6 PSCBS_0.30.0 RCurl_1.95-4.1 > XML_3.96-1.1 affyio_1.26.0 annotate_1.36.0 > bitops_1.0-4.2 > [8] digest_0.6.3 parallel_2.15.3 preprocessCore_1.20.0 > splines_2.15.3 stats4_2.15.3 survival_2.37-4 > tools_2.15.3 > [15] xtable_1.7-1 zlibbioc_1.4.0 > > > > > > -------------------------------------------------------------------- ------------------------- > Andreia J. Amaral, PhD > BioFIG - Center for Biodiversity, Functional and Integrative Genomics > Instituto de Medicina Molecular > University of Lisbon > Tel: +352 217500000 (ext. office: 28253) > email:andreiaamaral at fm.ul.pt ; andreiaamaral at fc.ul.pt > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor