Question: nsfilter error from expressionset obtained after using aroma for processing
0
gravatar for Andreia Fonseca
6.6 years ago by
Andreia Fonseca810 wrote:
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]]
ADD COMMENTlink modified 6.6 years ago by Wolfgang Huber13k • written 6.6 years ago by Andreia Fonseca810
Answer: nsfilter error from expressionset obtained after using aroma for processing
0
gravatar for Wolfgang Huber
6.6 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
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
ADD COMMENTlink written 6.6 years ago by Wolfgang Huber13k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 471 users visited in the last hour