Thank you, Jim. I tried featureNames(EsetData) <- gsub("_PM","", featureNames(EsetData)) annotation(EsetData) <- "hgu133plus2.db" And it solved a problem even though when I downloaded *hthgu133pluspm zip *from http://nmg-r.bioinformatics.nl/NuGO_R.html and installed it, it didn't. I am running the remainder of the code, it haven't given me errors so far. On Wed, Apr 17, 2013 at 12:23 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Zhenya, > > > On 4/17/2013 12:02 PM, Zhenya [guest] wrote: > >> Hi All, >> >> I am trying to run the code for GSVA (library with the same name). The >> code is below, but the main error is around annotation: >> >>> source("http://bioconductor.**org/biocLite.R<http: bioconductor.o="" rg="" bioclite.r=""> >>> ") >>> >> Bioconductor version 2.12 (BiocInstaller 1.10.0), ?biocLite for help >> >>> biocLite("hthgu133pluspm.db") >>> >> > There is no such package. You could easily create one yourself using the > AnnotationForge package (see the vignette). Or you could note that the > hthgu133pluspm array has identical content as the hgu133plus2 array, except > for a few extra control probesets, and the fact that they insisted on > adding an extra _PM to all the probesets. > > > sum(ls(hgu133plus2cdf) %in% gsub("_PM","", ls(hthgu133pluspmcdf))) > [1] 54675 > > length(ls(hgu133plus2cdf)) > [1] 54675 > > length(ls(hthgu133pluspmcdf)) > [1] 54715 > > ls(hthgu133pluspmcdf)[!gsub("_**PM","", ls(hthgu133pluspmcdf)) %in% > ls(hgu133plus2cdf)] > [1] "AFFX-NonspecificGC10_at" "AFFX-NonspecificGC11_at" > [3] "AFFX-NonspecificGC12_at" "AFFX-NonspecificGC13_at" > [5] "AFFX-NonspecificGC14_at" "AFFX-NonspecificGC15_at" > [7] "AFFX-NonspecificGC16_at" "AFFX-NonspecificGC17_at" > [9] "AFFX-NonspecificGC18_at" "AFFX-NonspecificGC19_at" > [11] "AFFX-NonspecificGC20_at" "AFFX-NonspecificGC21_at" > [13] "AFFX-NonspecificGC22_at" "AFFX-NonspecificGC23_at" > [15] "AFFX-NonspecificGC24_at" "AFFX-NonspecificGC25_at" > [17] "AFFX-NonspecificGC3_at" "AFFX-NonspecificGC4_at" > [19] "AFFX-NonspecificGC5_at" "AFFX-NonspecificGC6_at" > [21] "AFFX-NonspecificGC7_at" "AFFX-NonspecificGC8_at" > [23] "AFFX-NonspecificGC9_at" "AFFX-r2-TagA_at" > [25] "AFFX-r2-TagB_at" "AFFX-r2-TagC_at" > [27] "AFFX-r2-TagD_at" "AFFX-r2-TagE_at" > [29] "AFFX-r2-TagF_at" "AFFX-r2-TagG_at" > [31] "AFFX-r2-TagH_at" "AFFX-r2-TagIN-3_at" > [33] "AFFX-r2-TagIN-5_at" "AFFX-r2-TagIN-M_at" > [35] "AFFX-r2-TagJ-3_at" "AFFX-r2-TagJ-5_at" > [37] "AFFX-r2-TagO-3_at" "AFFX-r2-TagO-5_at" > [39] "AFFX-r2-TagQ-3_at" "AFFX-r2-TagQ-5_at" > > So you could either go to the trouble of building and installing a .db > package for this array, or you could do something like > > featureNames(EsetData) <- gsub("_PM","", featureNames(EsetData)) > annotation(EsetData) <- "hgu133plus2.db" > > and carry on as before. > > Best, > > Jim > > > BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0. >> Installing package(s) 'hthgu133pluspm.db' >> Warning message: >> package ‘hthgu133pluspm.db’ is not available (for R version 3.0.0) >> >> >> Code: >> >> # CREATE GeneSetCollection >> library(GSEABase) >> x<- scan("GeneSets.gmt", what="", sep="\n") >> GeneSets.gmt<- strsplit(x, "[[:space:]]+") >> names(GeneSets.gmt)<- sapply(GeneSets.gmt, `[[`, 1) >> GeneSets.gmt<- lapply(GeneSets.gmt, `[`, -1) >> n<- names(GeneSets.gmt) >> uniqueList<- lapply(GeneSets.gmt, unique) >> makeSet<- function(geneIds, n) {GeneSet(geneIds, >> geneIdType=SymbolIdentifier(), setName=n)} >> gsList<- gsc<- mapply(makeSet, uniqueList[], n) >> gsc<- GeneSetCollection(gsList) >> >> # DATASET >> # CREATE ExpressionSet >> exprs<- as.matrix(read.table("**ExprData.txt", header=TRUE, sep="\t", >> row.names=1, as.is=TRUE)) >> pData<- read.table("DesignFile.txt",**row.names=1, header=T,sep="\t") >> phenoData<- new("AnnotatedDataFrame",data=**pData) >> annotation<- "hthgu133pluspm.db" >> EsetData<- ExpressionSet(assayData=exprs,**phenoData=phenoData,** >> annotation="hthgu133pluspm") >> head(ExprData) >> >> #Gene Filtering >> library(genefilter) >> library("hthgu133pluspm") >> filtered_eset<- nsFilter(EsetData, require.entrez=TRUE, >> remove.dupEntrez=TRUE, var.func=IQR, var.filter=FALSE, var.cutoff=0.25, >> filterByQuantile=TRUE, feature.exclude="^AFFX") >> # get stats for numbers of probesets removed >> filtered_eset >> EsetData_f<- filtered_eset$eset >> >> # GSVA >> library(GSVA) >> gsva_es<- gsva(EsetData_f,gsc,abs.**ranking=FALSE,min.sz=1,max.sz=** >> 1000,mx.diff=TRUE)$es.obs >> >> I downloaded hthgu133pluspm from http://nmg-r.bioinformatics.** >> nl/NuGO_R.html <http: nmg-r.bioinformatics.nl="" nugo_r.html=""> >> and R still complains. The available on Bioconductor: >> hthgu133pluspmprobe >> and >> hthgu133pluspmcdf >> are not correct and give error for nsFilter and gsva: >> Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function ‘cols’ for >> signature ‘"environment"’ >> >> >> Mapping identifiers between gene sets and feature names >> Error in GeneSetCollection(lapply(what, mapIdentifiers, to, ..., verbose >> = verbose)) : >> error in evaluating the argument 'object' in selecting a method for >> function 'GeneSetCollection': Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function ‘cols’ for >> signature ‘"environment"’ >> >> >> >> Thank you, >> Zhenya >> >> -- output of sessionInfo(): >> >> R version 3.0.0 (2013-04-03) >> Platform: i386-w64-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] GSVA_1.8.0 BiocInstaller_1.10.0 >> hthgu133pluspmprobe_2.12.0 hthgu133pluspmcdf_2.12.0 genefilter_1.42.0 >> GSEABase_1.22.0 >> [7] graph_1.38.0 annotate_1.38.0 >> AnnotationDbi_1.22.1 Biobase_2.20.0 BiocGenerics_0.6.0 >> >> loaded via a namespace (and not attached): >> [1] DBI_0.2-5 IRanges_1.18.0 RSQLite_0.11.2 splines_3.0.0 >> stats4_3.0.0 survival_2.37-4 tools_3.0.0 XML_3.96-1.1 xtable_1.7-1 >> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]

Thank you, Jim. I tried featureNames(EsetData) <- gsub("_PM","", featureNames(EsetData)) annotation(EsetData) <- "hgu133plus2.db" And it solved a problem even though when I downloaded *hthgu133pluspm zip *from http://nmg-r.bioinformatics.nl/NuGO_R.html and installed it, it didn't. I am running the remainder of the code, it haven't given me errors so far. On Wed, Apr 17, 2013 at 12:23 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Zhenya, > > > On 4/17/2013 12:02 PM, Zhenya [guest] wrote: > >> Hi All, >> >> I am trying to run the code for GSVA (library with the same name). The >> code is below, but the main error is around annotation: >> >>> source("http://bioconductor.**org/biocLite.R<http: bioconductor.o="" rg="" bioclite.r=""> >>> ") >>> >> Bioconductor version 2.12 (BiocInstaller 1.10.0), ?biocLite for help >> >>> biocLite("hthgu133pluspm.db") >>> >> > There is no such package. You could easily create one yourself using the > AnnotationForge package (see the vignette). Or you could note that the > hthgu133pluspm array has identical content as the hgu133plus2 array, except > for a few extra control probesets, and the fact that they insisted on > adding an extra _PM to all the probesets. > > > sum(ls(hgu133plus2cdf) %in% gsub("_PM","", ls(hthgu133pluspmcdf))) > [1] 54675 > > length(ls(hgu133plus2cdf)) > [1] 54675 > > length(ls(hthgu133pluspmcdf)) > [1] 54715 > > ls(hthgu133pluspmcdf)[!gsub("_**PM","", ls(hthgu133pluspmcdf)) %in% > ls(hgu133plus2cdf)] > [1] "AFFX-NonspecificGC10_at" "AFFX-NonspecificGC11_at" > [3] "AFFX-NonspecificGC12_at" "AFFX-NonspecificGC13_at" > [5] "AFFX-NonspecificGC14_at" "AFFX-NonspecificGC15_at" > [7] "AFFX-NonspecificGC16_at" "AFFX-NonspecificGC17_at" > [9] "AFFX-NonspecificGC18_at" "AFFX-NonspecificGC19_at" > [11] "AFFX-NonspecificGC20_at" "AFFX-NonspecificGC21_at" > [13] "AFFX-NonspecificGC22_at" "AFFX-NonspecificGC23_at" > [15] "AFFX-NonspecificGC24_at" "AFFX-NonspecificGC25_at" > [17] "AFFX-NonspecificGC3_at" "AFFX-NonspecificGC4_at" > [19] "AFFX-NonspecificGC5_at" "AFFX-NonspecificGC6_at" > [21] "AFFX-NonspecificGC7_at" "AFFX-NonspecificGC8_at" > [23] "AFFX-NonspecificGC9_at" "AFFX-r2-TagA_at" > [25] "AFFX-r2-TagB_at" "AFFX-r2-TagC_at" > [27] "AFFX-r2-TagD_at" "AFFX-r2-TagE_at" > [29] "AFFX-r2-TagF_at" "AFFX-r2-TagG_at" > [31] "AFFX-r2-TagH_at" "AFFX-r2-TagIN-3_at" > [33] "AFFX-r2-TagIN-5_at" "AFFX-r2-TagIN-M_at" > [35] "AFFX-r2-TagJ-3_at" "AFFX-r2-TagJ-5_at" > [37] "AFFX-r2-TagO-3_at" "AFFX-r2-TagO-5_at" > [39] "AFFX-r2-TagQ-3_at" "AFFX-r2-TagQ-5_at" > > So you could either go to the trouble of building and installing a .db > package for this array, or you could do something like > > featureNames(EsetData) <- gsub("_PM","", featureNames(EsetData)) > annotation(EsetData) <- "hgu133plus2.db" > > and carry on as before. > > Best, > > Jim > > > BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0. >> Installing package(s) 'hthgu133pluspm.db' >> Warning message: >> package ‘hthgu133pluspm.db’ is not available (for R version 3.0.0) >> >> >> Code: >> >> # CREATE GeneSetCollection >> library(GSEABase) >> x<- scan("GeneSets.gmt", what="", sep="\n") >> GeneSets.gmt<- strsplit(x, "[[:space:]]+") >> names(GeneSets.gmt)<- sapply(GeneSets.gmt, `[[`, 1) >> GeneSets.gmt<- lapply(GeneSets.gmt, `[`, -1) >> n<- names(GeneSets.gmt) >> uniqueList<- lapply(GeneSets.gmt, unique) >> makeSet<- function(geneIds, n) {GeneSet(geneIds, >> geneIdType=SymbolIdentifier(), setName=n)} >> gsList<- gsc<- mapply(makeSet, uniqueList[], n) >> gsc<- GeneSetCollection(gsList) >> >> # DATASET >> # CREATE ExpressionSet >> exprs<- as.matrix(read.table("**ExprData.txt", header=TRUE, sep="\t", >> row.names=1, as.is=TRUE)) >> pData<- read.table("DesignFile.txt",**row.names=1, header=T,sep="\t") >> phenoData<- new("AnnotatedDataFrame",data=**pData) >> annotation<- "hthgu133pluspm.db" >> EsetData<- ExpressionSet(assayData=exprs,**phenoData=phenoData,** >> annotation="hthgu133pluspm") >> head(ExprData) >> >> #Gene Filtering >> library(genefilter) >> library("hthgu133pluspm") >> filtered_eset<- nsFilter(EsetData, require.entrez=TRUE, >> remove.dupEntrez=TRUE, var.func=IQR, var.filter=FALSE, var.cutoff=0.25, >> filterByQuantile=TRUE, feature.exclude="^AFFX") >> # get stats for numbers of probesets removed >> filtered_eset >> EsetData_f<- filtered_eset$eset >> >> # GSVA >> library(GSVA) >> gsva_es<- gsva(EsetData_f,gsc,abs.**ranking=FALSE,min.sz=1,max.sz=** >> 1000,mx.diff=TRUE)$es.obs >> >> I downloaded hthgu133pluspm from http://nmg-r.bioinformatics.** >> nl/NuGO_R.html <http: nmg-r.bioinformatics.nl="" nugo_r.html=""> >> and R still complains. The available on Bioconductor: >> hthgu133pluspmprobe >> and >> hthgu133pluspmcdf >> are not correct and give error for nsFilter and gsva: >> Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function ‘cols’ for >> signature ‘"environment"’ >> >> >> Mapping identifiers between gene sets and feature names >> Error in GeneSetCollection(lapply(what, mapIdentifiers, to, ..., verbose >> = verbose)) : >> error in evaluating the argument 'object' in selecting a method for >> function 'GeneSetCollection': Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function ‘cols’ for >> signature ‘"environment"’ >> >> >> >> Thank you, >> Zhenya >> >> -- output of sessionInfo(): >> >> R version 3.0.0 (2013-04-03) >> Platform: i386-w64-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] GSVA_1.8.0 BiocInstaller_1.10.0 >> hthgu133pluspmprobe_2.12.0 hthgu133pluspmcdf_2.12.0 genefilter_1.42.0 >> GSEABase_1.22.0 >> [7] graph_1.38.0 annotate_1.38.0 >> AnnotationDbi_1.22.1 Biobase_2.20.0 BiocGenerics_0.6.0 >> >> loaded via a namespace (and not attached): >> [1] DBI_0.2-5 IRanges_1.18.0 RSQLite_0.11.2 splines_3.0.0 >> stats4_3.0.0 survival_2.37-4 tools_3.0.0 XML_3.96-1.1 xtable_1.7-1 >> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]

Thank you, Robert. The previous suggestion worked, so it was related to annotation despite the fact that I manually installed it. I will use yours further on GSVA analyses! On Wed, Apr 17, 2013 at 12:24 PM, Robert Castelo <robert.castelo@upf.edu>wrote: > Dear Zhenya, > > from your output below i'd say that the problem arises when mapping > identifiers between the genes in gene sets from the 'GeneSetCollection' > object and the features from the 'ExpressionSet' object. > > my guess is that the problematic instruction would be this line, i'm > putting it here trying to use your variable names, please run it and paste > here the result: > > library(Biobase) > library(GSEABase) > > mapped.gset.idx.list <- mapIdentifiers(gsc, AnnoOrEntrezIdentifier(** > annotation(EsetData_f))) > > if this lines prompts an error, then in principle this is not as much of a > problem of GSVA but of how the identifier mapping magic should be working, > and maybe the maintainers of GSEABase can give you a hand there. > > please also paste the output of traceback() right after you get the error > and also the display of the objects 'gsc' and 'EsetData_f' > > > cheers, > robert. > > > On 04/17/2013 06:02 PM, Zhenya [guest] wrote: > >> >> Hi All, >> >> I am trying to run the code for GSVA (library with the same name). The >> code is below, but the main error is around annotation: >> >>> source("http://bioconductor.**org/biocLite.R<http: bioconductor.o="" rg="" bioclite.r=""> >>> ") >>> >> Bioconductor version 2.12 (BiocInstaller 1.10.0), ?biocLite for help >> >>> biocLite("hthgu133pluspm.db") >>> >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0. >> Installing package(s) 'hthgu133pluspm.db' >> Warning message: >> package ‘hthgu133pluspm.db’ is not available (for R version 3.0.0) >> >> >> Code: >> >> # CREATE GeneSetCollection >> library(GSEABase) >> x<- scan("GeneSets.gmt", what="", sep="\n") >> GeneSets.gmt<- strsplit(x, "[[:space:]]+") >> names(GeneSets.gmt)<- sapply(GeneSets.gmt, `[[`, 1) >> GeneSets.gmt<- lapply(GeneSets.gmt, `[`, -1) >> n<- names(GeneSets.gmt) >> uniqueList<- lapply(GeneSets.gmt, unique) >> makeSet<- function(geneIds, n) {GeneSet(geneIds, >> geneIdType=SymbolIdentifier(), setName=n)} >> gsList<- gsc<- mapply(makeSet, uniqueList[], n) >> gsc<- GeneSetCollection(gsList) >> >> # DATASET >> # CREATE ExpressionSet >> exprs<- as.matrix(read.table("**ExprData.txt", header=TRUE, sep="\t", >> row.names=1, as.is=TRUE)) >> pData<- read.table("DesignFile.txt",**row.names=1, header=T,sep="\t") >> phenoData<- new("AnnotatedDataFrame",data=**pData) >> annotation<- "hthgu133pluspm.db" >> EsetData<- ExpressionSet(assayData=exprs,**phenoData=phenoData,** >> annotation="hthgu133pluspm") >> head(ExprData) >> >> #Gene Filtering >> library(genefilter) >> library("hthgu133pluspm") >> filtered_eset<- nsFilter(EsetData, require.entrez=TRUE, >> remove.dupEntrez=TRUE, var.func=IQR, var.filter=FALSE, var.cutoff=0.25, >> filterByQuantile=TRUE, feature.exclude="^AFFX") >> # get stats for numbers of probesets removed >> filtered_eset >> EsetData_f<- filtered_eset$eset >> >> # GSVA >> library(GSVA) >> gsva_es<- gsva(EsetData_f,gsc,abs.**ranking=FALSE,min.sz=1,max.sz=** >> 1000,mx.diff=TRUE)$es.obs >> >> I downloaded hthgu133pluspm from http://nmg-r.bioinformatics.** >> nl/NuGO_R.html <http: nmg-r.bioinformatics.nl="" nugo_r.html=""> >> and R still complains. The available on Bioconductor: >> hthgu133pluspmprobe >> and >> hthgu133pluspmcdf >> are not correct and give error for nsFilter and gsva: >> Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function ‘cols’ for >> signature ‘"environment"’ >> >> Mapping identifiers between gene sets and feature names >> Error in GeneSetCollection(lapply(what, mapIdentifiers, to, ..., verbose >> = verbose)) : >> error in evaluating the argument 'object' in selecting a method for >> function 'GeneSetCollection': Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function ‘cols’ for >> signature ‘"environment"’ >> >> >> Thank you, >> Zhenya >> >> -- output of sessionInfo(): >> >> R version 3.0.0 (2013-04-03) >> Platform: i386-w64-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] GSVA_1.8.0 BiocInstaller_1.10.0 >> hthgu133pluspmprobe_2.12.0 hthgu133pluspmcdf_2.12.0 genefilter_1.42.0 >> GSEABase_1.22.0 >> [7] graph_1.38.0 annotate_1.38.0 >> AnnotationDbi_1.22.1 Biobase_2.20.0 BiocGenerics_0.6.0 >> >> loaded via a namespace (and not attached): >> [1] DBI_0.2-5 IRanges_1.18.0 RSQLite_0.11.2 splines_3.0.0 >> stats4_3.0.0 survival_2.37-4 tools_3.0.0 XML_3.96-1.1 xtable_1.7-1 >> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> > -- > Robert Castelo, PhD > Associate Professor > Dept. of Experimental and Health Sciences > Universitat Pompeu Fabra (UPF) > Barcelona Biomedical Research Park (PRBB) > Dr Aiguader 88 > E-08003 Barcelona, Spain > telf: +34.933.160.514 > fax: +34.933.160.550 > [[alternative HTML version deleted]]