Error message using arrayweights
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@richard-friedman-6273
Last seen 10.2 years ago
Dear List, I got the following error message in array weights: arrayw<-arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, tol = 1e-10) Error in arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, : convergence problem at gene 3021: array weights not estimable Here is the whole story: #################################################################### > library(affy) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ?BiocGenerics? The following objects are masked from ?package:parallel?: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ?package:stats?: xtabs The following objects are masked from ?package:base?: anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Warning message: '.find.package' is deprecated. Use 'find.package' instead. See help("Deprecated") > library(annaffy) Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: KEGG.db KEGG.db contains mappings based on older data because the original resource was removed from the the public domain before the most recent update was produced. This package should now be considered deprecated and future versions of Bioconductor may not have it available. Users who want more current data are encouraged to look at the KEGGREST or reactome.db packages > library(gcrma) > library(limma) > library(mouse4302.db) Loading required package: org.Mm.eg.db > raw<-ReadAffy() > gcrmanm<-gcrma(raw) Adjusting for optical effect............Done. Computing affinities.Done. Adjusting for non-specific binding............Done. Normalizing Calculating Expression > write.exprs(gcrmanm,"gloria2gcconexp.txt") > > > targets<-readTargets("targets.txt") > targets FileName Name mouse condition AA.het.con.01.01 AA.het.con.01.01.CEL AA.het.con.01.01 1 AA.het.con AA.het.con.02.03 AA.het.con.02.03.CEL AA.het.con.02.03 2 AA.het.con AA.het.con.05.09 AA.het.con.05.09.CEL AA.het.con.05.09 5 AA.het.con AA.het.con.06.11 AA.het.con.06.11.CEL AA.het.con.06.11 6 AA.het.con AA.het.con.11.21 AA.het.con.11.21.CEL AA.het.con.11.21 11 AA.het.con AA.het.con.12.23 AA.het.con.12.23.CEL AA.het.con.12.23 12 AA.het.con AB.het.sta.01.02 AB.het.sta.01.02.CEL AB.het.sta.01.02 1 AB.het.sta AB.het.sta.02.04 AB.het.sta.02.04.CEL AB.het.sta.02.04 2 AB.het.sta AB.het.sta.05.10 AB.het.sta.05.10.CEL AB.het.sta.05.10 5 AB.het.sta AB.het.sta.06.12 AB.het.sta.06.12.CEL AB.het.sta.06.12 6 AB.het.sta AB.het.sta.11.22 AB.het.sta.11.22.CEL AB.het.sta.11.22 11 AB.het.sta AB.het.sta.12.24 AB.het.sta.12.24.CEL AB.het.sta.12.24 12 AB.het.sta BA.mut.con.03.05 BA.mut.con.03.05.CEL BA.mut.con.03.05 3 BA.mut.con BA.mut.con.04.07 BA.mut.con.04.07.CEL BA.mut.con.04.07 4 BA.mut.con BA.mut.con.07.13 BA.mut.con.07.13.CEL BA.mut.con.07.13 7 BA.mut.con BA.mut.con.08.15 BA.mut.con.08.15.CEL BA.mut.con.08.15 8 BA.mut.con BA.mut.con.09.17 BA.mut.con.09.17.CEL BA.mut.con.09.17 9 BA.mut.con BB.mut.con.10.19 BB.mut.con.10.19.CEL BA.mut.con.10.19 10 BA.mut.con BB.mut.sta.03.06 BB.mut.sta.03.06.CEL BB.mut.sta.03.06 3 BB.mut.sta BB.mut.sta.04.08 BB.mut.sta.04.08.CEL BB.mut.sta.04.08 4 BB.mut.sta BB.mut.sta.07.14 BB.mut.sta.07.14.CEL BB.mut.sta.07.14 7 BB.mut.sta BB.mut.sta.08.16 BB.mut.sta.08.16.CEL BB.mut.sta.08.16 8 BB.mut.sta BB.mut.sta.09.18 BB.mut.sta.09.18.CEL BB.mut.sta.09.18 9 BB.mut.sta BB.mut.sta.10.20 BB.mut.sta.10.20.CEL BB.mut.sta.10.20 10 BB.mut.sta > condition<-factor(targets$condition,levels=c("AA.het.con","BA.mut.co n")) > condition [1] AA.het.con AA.het.con AA.het.con AA.het.con AA.het.con AA.het.con <na> <na> [9] <na> <na> <na> <na> BA.mut.con BA.mut.con BA.mut.con BA.mut.con [17] BA.mut.con BA.mut.con <na> <na> <na> <na> <na> <na> Levels: AA.het.con BA.mut.con > design<-model.matrix(~0+condition) > design conditionAA.het.con conditionBA.mut.con 1 1 0 2 1 0 3 1 0 4 1 0 5 1 0 6 1 0 13 0 1 14 0 1 15 0 1 16 0 1 17 0 1 18 0 1 attr(,"assign") [1] 1 1 attr(,"contrasts") attr(,"contrasts")$condition [1] "contr.treatment" > > colnames(design)<-c("AA.het.con","BA.mut.con") > > arrayw<-arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, tol = 1e-10) Error in arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, : convergence problem at gene 3021: array weights not estimable > fit<-lmFit(gcrmanm,design,weights=arrayw) Error in lm.series(y$exprs, design = design, ndups = ndups, spacing = spacing, : object 'arrayw' not found > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] mouse4302probe_2.12.0 mouse4302cdf_2.12.0 mouse4302.db_2.9.0 org.Mm.eg.db_2.9.0 [5] gcrma_2.32.0 annaffy_1.32.0 KEGG.db_2.9.1 GO.db_2.9.0 [9] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 affy_1.38.1 [13] Biobase_2.20.1 BiocGenerics_0.6.0 limma_3.16.8 BiocInstaller_1.10.4 loaded via a namespace (and not attached): [1] affyio_1.28.0 Biostrings_2.28.0 IRanges_1.18.4 preprocessCore_1.22.0 [5] splines_3.0.2 stats4_3.0.2 tools_3.0.2 zlibbioc_1.6.0 > #################################################################### When I try with reml I get the same error message: ################################################################ > arrayw<-arrayWeights(gcrmanm, design, method = "reml",maxiter = 50, tol = 1e-10) Error in arrayWeights(gcrmanm, design, method = "reml", maxiter = 50, : convergence problem at iteration 1: array weights not estimable > ###################################################################### I would appreciate any suggestions. Best wishes, Rich Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet)/ Columbia Department of Systems Biology Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman at c2b2.columbia.edu http://friedman.c2b2.columbia.edu/ In memoriam, Frederik Pohl
GO Cancer mouse4302 KEGGREST GO Cancer mouse4302 KEGGREST • 1.6k views
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Entering edit mode
Matthew Ritchie ▴ 1000
@matthew-ritchie-650
Last seen 7 months ago
Australia
Dear Rich, Thanks for the detailed example. If you send the data (offline) I can check what is going on in more detail. My suspicion is that you have a bunch of genes with identical values across all samples which leads to a convergence issue. You could try leaving out the arrayWeights() step, i.e. fit<-lmFit(gcrmanm,design) if you need results in a hurry. Best wishes, Matt ----- Original Message ----- From: "Richard Friedman" <friedman@c2b2.columbia.edu> To: "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> Sent: Thursday, 19 December, 2013 7:27:33 AM Subject: [BioC] Error message using arrayweights Dear List, I got the following error message in array weights: arrayw<-arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, tol = 1e-10) Error in arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, : convergence problem at gene 3021: array weights not estimable Here is the whole story: #################################################################### > library(affy) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ?BiocGenerics? The following objects are masked from ?package:parallel?: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ?package:stats?: xtabs The following objects are masked from ?package:base?: anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Warning message: '.find.package' is deprecated. Use 'find.package' instead. See help("Deprecated") > library(annaffy) Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: KEGG.db KEGG.db contains mappings based on older data because the original resource was removed from the the public domain before the most recent update was produced. This package should now be considered deprecated and future versions of Bioconductor may not have it available. Users who want more current data are encouraged to look at the KEGGREST or reactome.db packages > library(gcrma) > library(limma) > library(mouse4302.db) Loading required package: org.Mm.eg.db > raw<-ReadAffy() > gcrmanm<-gcrma(raw) Adjusting for optical effect............Done. Computing affinities.Done. Adjusting for non-specific binding............Done. Normalizing Calculating Expression > write.exprs(gcrmanm,"gloria2gcconexp.txt") > > > targets<-readTargets("targets.txt") > targets FileName Name mouse condition AA.het.con.01.01 AA.het.con.01.01.CEL AA.het.con.01.01 1 AA.het.con AA.het.con.02.03 AA.het.con.02.03.CEL AA.het.con.02.03 2 AA.het.con AA.het.con.05.09 AA.het.con.05.09.CEL AA.het.con.05.09 5 AA.het.con AA.het.con.06.11 AA.het.con.06.11.CEL AA.het.con.06.11 6 AA.het.con AA.het.con.11.21 AA.het.con.11.21.CEL AA.het.con.11.21 11 AA.het.con AA.het.con.12.23 AA.het.con.12.23.CEL AA.het.con.12.23 12 AA.het.con AB.het.sta.01.02 AB.het.sta.01.02.CEL AB.het.sta.01.02 1 AB.het.sta AB.het.sta.02.04 AB.het.sta.02.04.CEL AB.het.sta.02.04 2 AB.het.sta AB.het.sta.05.10 AB.het.sta.05.10.CEL AB.het.sta.05.10 5 AB.het.sta AB.het.sta.06.12 AB.het.sta.06.12.CEL AB.het.sta.06.12 6 AB.het.sta AB.het.sta.11.22 AB.het.sta.11.22.CEL AB.het.sta.11.22 11 AB.het.sta AB.het.sta.12.24 AB.het.sta.12.24.CEL AB.het.sta.12.24 12 AB.het.sta BA.mut.con.03.05 BA.mut.con.03.05.CEL BA.mut.con.03.05 3 BA.mut.con BA.mut.con.04.07 BA.mut.con.04.07.CEL BA.mut.con.04.07 4 BA.mut.con BA.mut.con.07.13 BA.mut.con.07.13.CEL BA.mut.con.07.13 7 BA.mut.con BA.mut.con.08.15 BA.mut.con.08.15.CEL BA.mut.con.08.15 8 BA.mut.con BA.mut.con.09.17 BA.mut.con.09.17.CEL BA.mut.con.09.17 9 BA.mut.con BB.mut.con.10.19 BB.mut.con.10.19.CEL BA.mut.con.10.19 10 BA.mut.con BB.mut.sta.03.06 BB.mut.sta.03.06.CEL BB.mut.sta.03.06 3 BB.mut.sta BB.mut.sta.04.08 BB.mut.sta.04.08.CEL BB.mut.sta.04.08 4 BB.mut.sta BB.mut.sta.07.14 BB.mut.sta.07.14.CEL BB.mut.sta.07.14 7 BB.mut.sta BB.mut.sta.08.16 BB.mut.sta.08.16.CEL BB.mut.sta.08.16 8 BB.mut.sta BB.mut.sta.09.18 BB.mut.sta.09.18.CEL BB.mut.sta.09.18 9 BB.mut.sta BB.mut.sta.10.20 BB.mut.sta.10.20.CEL BB.mut.sta.10.20 10 BB.mut.sta > condition<-factor(targets$condition,levels=c("AA.het.con","BA.mut.co n")) > condition [1] AA.het.con AA.het.con AA.het.con AA.het.con AA.het.con AA.het.con <na> <na> [9] <na> <na> <na> <na> BA.mut.con BA.mut.con BA.mut.con BA.mut.con [17] BA.mut.con BA.mut.con <na> <na> <na> <na> <na> <na> Levels: AA.het.con BA.mut.con > design<-model.matrix(~0+condition) > design conditionAA.het.con conditionBA.mut.con 1 1 0 2 1 0 3 1 0 4 1 0 5 1 0 6 1 0 13 0 1 14 0 1 15 0 1 16 0 1 17 0 1 18 0 1 attr(,"assign") [1] 1 1 attr(,"contrasts") attr(,"contrasts")$condition [1] "contr.treatment" > > colnames(design)<-c("AA.het.con","BA.mut.con") > > arrayw<-arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, tol = 1e-10) Error in arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, : convergence problem at gene 3021: array weights not estimable > fit<-lmFit(gcrmanm,design,weights=arrayw) Error in lm.series(y$exprs, design = design, ndups = ndups, spacing = spacing, : object 'arrayw' not found > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] mouse4302probe_2.12.0 mouse4302cdf_2.12.0 mouse4302.db_2.9.0 org.Mm.eg.db_2.9.0 [5] gcrma_2.32.0 annaffy_1.32.0 KEGG.db_2.9.1 GO.db_2.9.0 [9] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 affy_1.38.1 [13] Biobase_2.20.1 BiocGenerics_0.6.0 limma_3.16.8 BiocInstaller_1.10.4 loaded via a namespace (and not attached): [1] affyio_1.28.0 Biostrings_2.28.0 IRanges_1.18.4 preprocessCore_1.22.0 [5] splines_3.0.2 stats4_3.0.2 tools_3.0.2 zlibbioc_1.6.0 > #################################################################### When I try with reml I get the same error message: ################################################################ > arrayw<-arrayWeights(gcrmanm, design, method = "reml",maxiter = 50, tol = 1e-10) Error in arrayWeights(gcrmanm, design, method = "reml", maxiter = 50, : convergence problem at iteration 1: array weights not estimable > ###################################################################### I would appreciate any suggestions. Best wishes, Rich Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet)/ Columbia Department of Systems Biology Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman at c2b2.columbia.edu http://friedman.c2b2.columbia.edu/ In memoriam, Frederik Pohl _______________________________________________ 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}
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