Dear list, sorry to bother you, but I'm experiencing some problem in using GOstats package. I'm trying to find the enrichment in GO family of a set of genes for which I have the LocusLink ID in a txt file. When I reach the point of using makeGOGraph I encounter this error message: Error in clearNode(node, object) : NA is not a node in the graph I'm using R 2.0.1 and bioconductor 1.5 Here is the script I'm running: > require(GO) Loading required package: GO [1] TRUE > require(graph) Loading required package: graph Loading required package: cluster Loading required package: Ruuid Creating a new generic function for "print" in "Ruuid" Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. [1] TRUE > require(GOstats) Loading required package: GOstats Loading required package: annotate Loading required package: RBGL Loading required package: xtable Attaching package 'xtable': The following object(s) are masked from package:graph : label Loading required package: genefilter Loading required package: survival Loading required package: splines Loading required package: multtest Loading required package: reposTools Loading required package: hgu95av2 [1] TRUE > require(annotate) [1] TRUE > gNsel<-geneNames(diffexpr.iqr.rma) # diffexpr.iqr.rma is a txt file with a list of LocusLink IDs > my.go<-"BP" > p.value<-0.01 > gNsLL <- as.character(unique(unlist(mget(gNsel, env=hgu133plus2LOCUSID, ifnotfound=NA)))) > gGhyp <- GOHyperG(gNsLL, lib="hgu133plus2", what=my.go) > gGO <- makeGOGraph(gNsLL, my.go) Error in clearNode(node, object) : NA is not a node in the graph Have anybody encountered a similar problem? Thanks, Roberta ********************************************************************** ****** *** DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information contai...{{dropped}}

On Feb 14, 2005, at 12:26 AM, Bosotti, Roberta [Nervianoms] wrote: > Dear list, > > sorry to bother you, but I'm experiencing some problem in using GOstats > package. I'm trying to find the enrichment in GO family of a set of > genes > for which I have the LocusLink ID in a txt file. > When I reach the point of using makeGOGraph I encounter this error > message: > > Error in clearNode(node, object) : NA is not a node in the graph > > I'm using R 2.0.1 and bioconductor 1.5 > Here is the script I'm running: > >> require(GO) > Loading required package: GO > [1] TRUE >> require(graph) > Loading required package: graph > Loading required package: cluster > Loading required package: Ruuid > Creating a new generic function for "print" in "Ruuid" > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > [1] TRUE >> require(GOstats) > Loading required package: GOstats > Loading required package: annotate > Loading required package: RBGL > Loading required package: xtable > > Attaching package 'xtable': > > > The following object(s) are masked from package:graph : > > label > > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Loading required package: multtest > Loading required package: reposTools > > Loading required package: hgu95av2 > [1] TRUE >> require(annotate) > [1] TRUE >> gNsel<-geneNames(diffexpr.iqr.rma) # diffexpr.iqr.rma is a txt file >> with a > list of LocusLink IDs >> my.go<-"BP" >> p.value<-0.01 >> gNsLL <- as.character(unique(unlist(mget(gNsel, >> env=hgu133plus2LOCUSID, > ifnotfound=NA)))) You might want to remove the NA's in gNsLL at this point. >> gGhyp <- GOHyperG(gNsLL, lib="hgu133plus2", what=my.go) >> gGO <- makeGOGraph(gNsLL, my.go) What version of GO and of GOstats are you using(please try to report version numbers for R and packages when reporting errors)? If they are the most recent, then we might need to have a copy of gNsLL in order to track down the problem. Robert > Error in clearNode(node, object) : NA is not a node in the graph > > Have anybody encountered a similar problem? > > Thanks, Roberta > > > ******************************************************************** *** > ***** > *** > DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information > contai...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+

Hi Roberta, I had a similar problem recently, and it turned out to be a matter of versioning between the GOstats package and GO package. There have been some changes in the way data is presented in the GO package, which required a tiny but important modification in makeGOGraph. Make sure to use the most recent versions of both, and let me know if that helps. For me it works with GO 1.6.8 GOstats 1.1.2 Best wishes Wolfgang Bosotti, Roberta [Nervianoms] wrote: > Dear list, > > sorry to bother you, but I'm experiencing some problem in using GOstats > package. I'm trying to find the enrichment in GO family of a set of genes > for which I have the LocusLink ID in a txt file. > When I reach the point of using makeGOGraph I encounter this error message: > > Error in clearNode(node, object) : NA is not a node in the graph > > I'm using R 2.0.1 and bioconductor 1.5 > Here is the script I'm running: > > >>require(GO) > > Loading required package: GO > [1] TRUE > >>require(graph) > > Loading required package: graph > Loading required package: cluster > Loading required package: Ruuid > Creating a new generic function for "print" in "Ruuid" > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > [1] TRUE > >>require(GOstats) > > Loading required package: GOstats > Loading required package: annotate > Loading required package: RBGL > Loading required package: xtable > > Attaching package 'xtable': > > > The following object(s) are masked from package:graph : > > label > > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Loading required package: multtest > Loading required package: reposTools > > Loading required package: hgu95av2 > [1] TRUE > >>require(annotate) > > [1] TRUE > >>gNsel<-geneNames(diffexpr.iqr.rma) # diffexpr.iqr.rma is a txt file with a > > list of LocusLink IDs > >>my.go<-"BP" >> p.value<-0.01 >>gNsLL <- as.character(unique(unlist(mget(gNsel, env=hgu133plus2LOCUSID, > > ifnotfound=NA)))) > >>gGhyp <- GOHyperG(gNsLL, lib="hgu133plus2", what=my.go) >>gGO <- makeGOGraph(gNsLL, my.go) > > Error in clearNode(node, object) : NA is not a node in the graph > > Have anybody encountered a similar problem? > > Thanks, Roberta > > > ******************************************************************** ******** > *** > DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information contai...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber

Dear Robert, thanks for your reply. I'm using 1.6.8 version of GO and 1.1.1 version of GOstats. I noticed that there is one "NA" in the gNsLL list, this might be the reson of the error. Roberta -----Original Message----- From: Robert Gentleman [mailto:rgentlem@fhcrc.org] Sent: Monday, February 14, 2005 9:34 AM To: Bosotti, Roberta [Nervianoms] Cc: 'bioconductor@stat.math.ethz.ch' Subject: Re: [BioC] makeGOGraph error On Feb 14, 2005, at 12:26 AM, Bosotti, Roberta [Nervianoms] wrote: > Dear list, > > sorry to bother you, but I'm experiencing some problem in using GOstats > package. I'm trying to find the enrichment in GO family of a set of > genes > for which I have the LocusLink ID in a txt file. > When I reach the point of using makeGOGraph I encounter this error > message: > > Error in clearNode(node, object) : NA is not a node in the graph > > I'm using R 2.0.1 and bioconductor 1.5 > Here is the script I'm running: > >> require(GO) > Loading required package: GO > [1] TRUE >> require(graph) > Loading required package: graph > Loading required package: cluster > Loading required package: Ruuid > Creating a new generic function for "print" in "Ruuid" > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > [1] TRUE >> require(GOstats) > Loading required package: GOstats > Loading required package: annotate > Loading required package: RBGL > Loading required package: xtable > > Attaching package 'xtable': > > > The following object(s) are masked from package:graph : > > label > > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Loading required package: multtest > Loading required package: reposTools > > Loading required package: hgu95av2 > [1] TRUE >> require(annotate) > [1] TRUE >> gNsel<-geneNames(diffexpr.iqr.rma) # diffexpr.iqr.rma is a txt file >> with a > list of LocusLink IDs >> my.go<-"BP" >> p.value<-0.01 >> gNsLL <- as.character(unique(unlist(mget(gNsel, >> env=hgu133plus2LOCUSID, > ifnotfound=NA)))) You might want to remove the NA's in gNsLL at this point. >> gGhyp <- GOHyperG(gNsLL, lib="hgu133plus2", what=my.go) >> gGO <- makeGOGraph(gNsLL, my.go) What version of GO and of GOstats are you using(please try to report version numbers for R and packages when reporting errors)? If they are the most recent, then we might need to have a copy of gNsLL in order to track down the problem. Robert > Error in clearNode(node, object) : NA is not a node in the graph > > Have anybody encountered a similar problem? > > Thanks, Roberta > > > ******************************************************************** *** > ***** > *** > DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information > contai...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+ ********************************************************************** ****** *** DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information contai...{{dropped}}

Hi list, just drop a line to update you on the issue I had with makeGOGraph. The problem was due to the old version of GOstats I was using (1.1.1). I updated as Wolfgang suggested to version 1.1.2 and it works fine. Many thanks to Wolfgang and Robert for the help! Roberta -----Original Message----- From: Wolfgang Huber [mailto:huber@ebi.ac.uk] Sent: Monday, February 14, 2005 9:20 AM To: Bosotti, Roberta [Nervianoms] Cc: 'bioconductor@stat.math.ethz.ch' Subject: Re: [BioC] makeGOGraph error Hi Roberta, I had a similar problem recently, and it turned out to be a matter of versioning between the GOstats package and GO package. There have been some changes in the way data is presented in the GO package, which required a tiny but important modification in makeGOGraph. Make sure to use the most recent versions of both, and let me know if that helps. For me it works with GO 1.6.8 GOstats 1.1.2 Best wishes Wolfgang Bosotti, Roberta [Nervianoms] wrote: > Dear list, > > sorry to bother you, but I'm experiencing some problem in using GOstats > package. I'm trying to find the enrichment in GO family of a set of genes > for which I have the LocusLink ID in a txt file. > When I reach the point of using makeGOGraph I encounter this error message: > > Error in clearNode(node, object) : NA is not a node in the graph > > I'm using R 2.0.1 and bioconductor 1.5 > Here is the script I'm running: > > >>require(GO) > > Loading required package: GO > [1] TRUE > >>require(graph) > > Loading required package: graph > Loading required package: cluster > Loading required package: Ruuid > Creating a new generic function for "print" in "Ruuid" > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > [1] TRUE > >>require(GOstats) > > Loading required package: GOstats > Loading required package: annotate > Loading required package: RBGL > Loading required package: xtable > > Attaching package 'xtable': > > > The following object(s) are masked from package:graph : > > label > > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Loading required package: multtest > Loading required package: reposTools > > Loading required package: hgu95av2 > [1] TRUE > >>require(annotate) > > [1] TRUE > >>gNsel<-geneNames(diffexpr.iqr.rma) # diffexpr.iqr.rma is a txt file with a > > list of LocusLink IDs > >>my.go<-"BP" >> p.value<-0.01 >>gNsLL <- as.character(unique(unlist(mget(gNsel, env=hgu133plus2LOCUSID, > > ifnotfound=NA)))) > >>gGhyp <- GOHyperG(gNsLL, lib="hgu133plus2", what=my.go) >>gGO <- makeGOGraph(gNsLL, my.go) > > Error in clearNode(node, object) : NA is not a node in the graph > > Have anybody encountered a similar problem? > > Thanks, Roberta > > > ********************************************************************** ****** > *** > DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information contai...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber ------------------------------------- ********************************************************************** ****** *** DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information contai...{{dropped}}