Hi Robert, Following is the information you asked for: > traceback() 7: match(x, y) 6: na.omit(match(x, y)) 5: FUN(X[[1L]], ...) 4: lapply(gset.idx.list, function(x, y) na.omit(match(x, y)), rownames(expr)) 3: .local(expr, gset.idx.list, ...) 2: gsva(data.m, c3gsc2, abs.ranking = TRUE, min.sz = 1, max.sz = Inf, no.bootstraps = 0, bootstrap.percent = 0.632, parallel.sz = 0, parallel.type = "SOCK", verbose = TRUE, mx.diff = TRUE) 1: gsva(data.m, c3gsc2, abs.ranking = TRUE, min.sz = 1, max.sz = Inf, no.bootstraps = 0, bootstrap.percent = 0.632, parallel.sz = 0, parallel.type = "SOCK", verbose = TRUE, mx.diff = TRUE) > sessionInfo () R version 2.13.1 (2011-07-08) Platform: i386-pc-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] stats graphics grDevices utils datasets methods base other attached packages: [1] GSVA_1.0.1 RColorBrewer_1.0-5 limma_3.8.3 genefilter_1.34.0 GSEABase_1.14.0 graph_1.30.0 annotate_1.30.1 [8] AnnotationDbi_1.14.1 Biobase_2.12.2 loaded via a namespace (and not attached): [1] DBI_0.2-5 RSQLite_0.10.0 splines_2.13.1 survival_2.36-10 tools_2.13.1 XML_3.4-2.2 xtable_1.6-0 Looking forward to your reply. Best Regards, Som. > Date: Wed, 16 Nov 2011 22:04:06 +0100 > From: robert.castelo@upf.edu > To: genome1976@hotmail.com > CC: bioconductor@r-project.org > Subject: Re: [BioC] GSVA: using Entrez ID's as identifiers > > hi Som, > > i'm cc'ing the BioC mailing list, please remember to do it when you > answer since this works as a knowledge base for everyone else. > > i'd need two bits of information from you to find out what might be > happening: one, right after the error pops up, please write in the R shell: > > traceback() > > and paste here the output of this function. > > two, please paste also here the ouput of > > sessionInfo() > > > both steps are in fact recommended by the BioC mailinglist posting guide: > > http://www.bioconductor.org/help/mailing-list/posting-guide > > robert. > > On 11/16/11 9:04 PM, somnath bandyopadhyay wrote: > > Hi Robert, > > > > I am trying to use GSVA on a microarray dataset and I am trying to use > > one of the Broad gene set collections for the enrichment purposes. > > > > > > library(GSEABase) > > library(Biobase) > > library(genefilter) > > library(limma) > > library(RColorBrewer) > > library(graph) > > library(GSVA) > > > > c3gsc2 <- > > getGmt("c2.cp.kegg.v3.0.entrez.gmt",collectionType=BroadCollection(category="c3"),geneIdType=EntrezIdentifier()) > > class(c3gsc2) > > c3gsc2 > > > > data <- read.table("gsva_infliximab_data.txt", header=T, row.names=1, > > sep="\t")# the data matrix is filtered for low expressors etc. and I am > > using Entrez Gene ID as row identifiers. > > class(data) > > data.m <- as.matrix(data) > > > > new <- gsva(data.m, > > c3gsc2,abs.ranking=TRUE,min.sz=1,max.sz=Inf,no.bootstraps=0,bootstrap.percent > > = .632,parallel.sz=0,parallel.type="SOCK",verbose=TRUE,mx.diff=TRUE) > > > > > > I keep getting the following error at this step > > Error in match(x, y) : 'match' requires vector arguments > > > > Could you pleaase tell me what I am doing wrong? > > > > Thanks so much, > > Som. > > > > > > > > > > > > > > > > > > > From: robert.castelo@upf.edu > > > To: kellert@ohsu.edu > > > Date: Wed, 16 Nov 2011 08:43:48 +0100 > > > CC: wendy2.qiao@gmail.com; bioconductor@r-project.org > > > Subject: Re: [BioC] GSVA: using Entrez ID's as identifiers > > > > > > hi Tom, > > > > > > i'm a bit unsure what are you asking in relationship with this thread, > > > but i guess you're interested in creating a custom annotation package. > > > For that purpose i'd recommend you to read through the vignettes of the > > > AnnotationDbi package. i'm not an expert in creating custom annotation > > > packages so if you encounter problems to go ahead i think you should > > > start a new thread with the specific question or problem you want to > > > solve. > > > > > > cheers, > > > robert. > > > > > > On Tue, 2011-11-15 at 14:24 -0800, Tom Keller wrote: > > > > Greetings, > > > > The annotation for the miRNA chip does not seem to have the same > > amount of > > > > information as the hgu95 db. Is there some help available for > > mapping miRNA > > > > probes to their target genes? > > > > > > > > thanks > > > > Thomas (Tom) Keller, PhD > > > > kellert at ohsu.edu > > > > 503.494.2442 > > > > 6588 R Jones Hall (BSc/CROET) > > > > MMI DNA Services > > > > Member of OHSU Shared Resources > > > > > > > > On Nov 14, 2011, at 11:28 PM, Robert Castelo wrote: > > > > > > > > > hi Wendy, > > > > > > > > > > i'm afraid you need to get a little bit acquainted with the way > > in which > > > > > annotations are handled in BioC. a good starting point could be > > looking > > > > > a the vignette "AnnotationDbi: How to use the .db annotation > > packages" > > > > > from the AnnotationDbi package. > > > > > > > > > > the short answer to your problem is that hgu95a is not the only > > platform > > > > > for which annotations exist in BioC, basically there is an annotation > > > > > package for each platform supported by BioC (you can look all of > > them up > > > > > by going to > > http://www.bioconductor.org/packages/release/BiocViews.html > > > > > and clicking on "AnnotationData") but in order to use on such > > annotation > > > > > packages you need > > > > > > > > > > 1. install it once in your system via source() and biocLite() just as > > > > > with every software package > > > > > > > > > > 2. load it via the library() function. > > > > > > > > > > in order to use the human organism-level package i mentioned in my > > > > > previous email you need to install it first and then load it > > prior to do > > > > > anything else with it. > > > > > > > > > > let me know if this still does not solve your problem. > > > > > > > > > > cheers, > > > > > robert. > > > > > > > > > > On Mon, 2011-11-14 at 18:40 -0500, Wendy Qiao wrote: > > > > >> Hi Robert, > > > > >> > > > > >> Thank you for your reply. I happened to convert all the genes to > > > > >> hgu95a probe IDs as I found that this is the only platform that > > works > > > > >> with ExpressionSet. It would be great that we could make the > > entrez ID > > > > >> works. Following is my error that I got with your code. > > > > >> > > > > >> > > > > >> Thank you. > > > > >> Wendy > > > > >> > > > > >> > > > > >>> BcellSet > > > > >> ExpressionSet (storageMode: lockedEnvironment) > > > > >> assayData: 12148 features, 7 samples > > > > >> element names: exprs > > > > >> protocolData: none > > > > >> phenoData > > > > >> sampleNames: Illumi_PREBCEL_1 Illumi_PREBCEL_2 ... Affy_PREBCEL_4 (7 > > > > >> total) > > > > >> varLabels: CellType Platform Replicates > > > > >> varMetadata: labelDescription > > > > >> featureData: none > > > > >> experimentData: use 'experimentData(object)' > > > > >> Annotation: org.Hs.eg.db > > > > >>> > > > > >> > > preBcell.KEGG<-gsva(BcellSet,KEGGc2BroadSets,abs.ranking=FALSE)$es.obs > > > > >> 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 get(mapName, envir = pkgEnv, > > > > >> inherits = FALSE) : > > > > >> object 'org.Hs.egENTREZID' not found > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> On 14 November 2011 12:27, Robert Castelo > > > > >> wrote: > > > > >> hi Wendy, > > > > >> > > > > >> sorry for my late answer. in principle there is no problem for > > > > >> the > > > > >> gsva() function to take Entrez IDs in your expression data > > > > >> matrix. > > > > >> > > > > >> if the expression data comes as a matrix, and rows are > > > > >> annotated with > > > > >> Entrez IDs and the gene sets are also annotated with Entrez > > > > >> IDs, there > > > > >> should be absolutely no problem. > > > > >> > > > > >> if the expression data comes as an ExpressionSet object where > > > > >> the > > > > >> 'features' are not Affy probe IDs but just EntrezIDs. just > > > > >> make sure > > > > >> that the annotation slot has the corresponding organism-level > > > > >> package. > > > > >> for instance, in the case of human: > > > > >> > > > > >> annotation(eset) <- "org.Hs.eg.db" > > > > >> > > > > >> let me know if you have any problem with this. > > > > >> > > > > >> cheers, > > > > >> robert. > > > > >> > > > > >> On Fri, 2011-11-11 at 14:44 -0500, Wendy Qiao wrote: > > > > >>> Hi all, > > > > >>> > > > > >>> I am using the GSVA package for some analysis. I found that > > > > >> the package > > > > >>> only takes the gene expression matrix annotated with > > > > >> affymetrix probe IDs, > > > > >>> although the gene set collection is made of Entrez IDs. I > > > > >> imagine there a > > > > >>> step in the package for converting the Affymetrix probe IDs > > > > >> to Entrez IDs. > > > > >>> As my data are from the Illumina platform, I am wondering if > > > > >> an expression > > > > >>> matrix annotated with Entrez IDs can be used directly. > > > > >>> > > > > >>> Thank you, > > > > >>> Wendy > > > > >>> > > > > >> > > > > >>> [[alternative HTML version deleted]] > > > > >>> > > > > >>> _______________________________________________ > > > > >>> Bioconductor mailing list > > > > >>> Bioconductor@r-project.org > > > > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > >>> Search the archives: > > > > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > >>> > > > > >> > > > > >> > > > > >> > > > > >> > > > > > > > > > > _______________________________________________ > > > > > Bioconductor mailing list > > > > > Bioconductor@r-project.org > > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]