I am getting error messages while using GOhyperG. The first is when I try to pass along a list of LL identifiers that has duplicate entries. I get a message that says that the list must be unique. This is solved my using the unique() function. The vignette, however, seems to say that the function automatically takes into account the non-uniqueness of the identifiers. Is this just in relation to the annotation environment, not the user list? The second is more serious and I don't know how to correct it. I am using the annotation package rat2302 and get "Error: value for 'M18349cds#1_s_at' not found". Using options recover I get: Enter a frame number, or 0 to exit 1: GOHyperG.BP.MF.CC.func(x = unique(LL.vec[200:500]), annot.pckg) 2: GOHyperG(x, lib = annot.pckg, what = "BP") 3: sapply(goV, function(x) { 4: lapply(as.list(X), FUN, ...) 5: FUN(X[[1]], ...) 6: unique(unlist(mget(x, getDataEnv("LOCUSID", lib)))) 7: unlist(mget(x, getDataEnv("LOCUSID", lib))) 8: mget(x, getDataEnv("LOCUSID", lib)) 9: function (x) Selection: 9 Called from: eval(expr, envir, enclos) Browse[1]> x [1] "M18349cds#1_s_at" It seems that the annotation package may have an error or something. Am I doing something wrong? Is there a fix for this? Thanks, Mark Mark W. Kimpel MD ? Official Business Address: ? Department of Psychiatry Indiana University School of Medicine Biotechnology, Research, & Training Center 1345 W. 16th Street Indianapolis, IN 46202 ? Preferred Mailing Address: ? 15032 Hunter Court Westfield, IN? 46074 ? (317) 490-5129 Home, Work, & Mobile 1-(317)-536-2730 FAX

Hi, The posting guide does ask you to provide the output of sessionInfo, as well as examples that can be cut and pasted. Kimpel, Mark William wrote: > I am getting error messages while using GOhyperG. > > The first is when I try to pass along a list of LL identifiers that has duplicate entries. I get a message that says that the list must be unique. This is solved my using the unique() function. The vignette, however, seems to say that the function automatically takes into account the non-uniqueness of the identifiers. Is this just in relation to the annotation environment, not the user list? The manual page is unequivocal: ?GOhyerG says (among other things) Usage: GOHyperG(x, lib="hgu95av2", what="MF") Arguments: x: A vector of unique LocusLink identifiers. Manual pages are where you should look for this sort of information. If you give a specific set of line numbers for the part of the vignette that seems to be in error, I will fix it to align with the manual page. Best wishes, Robert ps the second questions seems to have already been addressed > > The second is more serious and I don't know how to correct it. I am using the annotation package rat2302 and get "Error: value for 'M18349cds#1_s_at' not found". Using options recover I get: > > > Enter a frame number, or 0 to exit > > 1: GOHyperG.BP.MF.CC.func(x = unique(LL.vec[200:500]), annot.pckg) > 2: GOHyperG(x, lib = annot.pckg, what = "BP") > 3: sapply(goV, function(x) { > 4: lapply(as.list(X), FUN, ...) > 5: FUN(X[[1]], ...) > 6: unique(unlist(mget(x, getDataEnv("LOCUSID", lib)))) > 7: unlist(mget(x, getDataEnv("LOCUSID", lib))) > 8: mget(x, getDataEnv("LOCUSID", lib)) > 9: function (x) > > Selection: 9 > Called from: eval(expr, envir, enclos) > Browse[1]> x > [1] "M18349cds#1_s_at" > > It seems that the annotation package may have an error or something. > > Am I doing something wrong? Is there a fix for this? > > Thanks, > > Mark > > > Mark W. Kimpel MD > > Official Business Address: > > Department of Psychiatry > Indiana University School of Medicine > Biotechnology, Research, & Training Center > 1345 W. 16th Street > Indianapolis, IN 46202 > > Preferred Mailing Address: > > 15032 Hunter Court > Westfield, IN 46074 > > (317) 490-5129 Home, Work, & Mobile > 1-(317)-536-2730 FAX > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Hi Mark, Can you post the output of sessionInfo() so we can see the versions of annotation and other packages you have? + seth

>The second is more serious and I don't know how to correct it. I am using the annotation package rat2302 and get "Error: value for 'M18349cds#1_s_at' not found". Using options recover I get: Looks like you were trying to look up probe id "M18349cds#1_s_at" that does not belong to rat2302. > > >Enter a frame number, or 0 to exit > >1: GOHyperG.BP.MF.CC.func(x = unique(LL.vec[200:500]), annot.pckg) >2: GOHyperG(x, lib = annot.pckg, what = "BP") >3: sapply(goV, function(x) { >4: lapply(as.list(X), FUN, ...) >5: FUN(X[[1]], ...) >6: unique(unlist(mget(x, getDataEnv("LOCUSID", lib)))) >7: unlist(mget(x, getDataEnv("LOCUSID", lib))) >8: mget(x, getDataEnv("LOCUSID", lib)) >9: function (x) > >Selection: 9 >Called from: eval(expr, envir, enclos) >Browse[1]> x >[1] "M18349cds#1_s_at" > >It seems that the annotation package may have an error or something. > >Am I doing something wrong? Is there a fix for this? > >Thanks, > >Mark > > >Mark W. Kimpel MD >? >Official Business Address: >? >Department of Psychiatry >Indiana University School of Medicine >Biotechnology, Research, & Training Center >1345 W. 16th Street >Indianapolis, IN 46202 >? >Preferred Mailing Address: >? >15032 Hunter Court >Westfield, IN? 46074 >? >(317) 490-5129 Home, Work, & Mobile >1-(317)-536-2730 FAX > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

I am still getting an Error Message when I use GOHyperG. The message reads, "Error: value for 'L00981mRNA#2_at' not found". As you can see from my script below, which replicates this error, that this Affy ID is not on my original list. Please see my script below the sessionInfo to replicate the error. Note that in my original post I mistakenly said that I am using rat2302; I am actually using rgu34a. Thanks, Mark ###################################################################### ## #### My session info is: R version 2.2.0, 2005-08-29, i386-pc-mingw32 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: hgu95av2 GOstats genefilter xtable RBGL annotate GO graph Ruuid cluster rgu34a limma rgu34acdf multtest "1.6.5" "1.2.0" "1.7.7" "1.2-5" "1.4.0" "1.6.3" "1.6.5" "1.6.5" "1.6.2" "1.10.1" "1.8.5" "2.0.7" "1.4.3" "1.7.3" survival affy reposTools Biobase "2.18" "1.7.2" "1.6.2" "1.7.0" ###################################################################### ## #### require(GOstats) affyIDVec<- c("AB000362_at", "AB000517_s_at", "AB001453_at", "AB001576_s_at", "AB002086_at") annot.pckg<-"rgu34a" LocusLinkVec<-c(rep(NA,length(affyIDVec))) #map Affy IDs to Locus Link IDs for (i in 1:length(affyIDVec)) { LocusLinkVec[i]<-if(!is.na(unlist(mget(x=affyIDVec[i], envir=get(paste(annot.pckg, "LOCUSID", sep = "")), mode = "any", ifnotfound = NA, inherits = FALSE)))){unlist(mget(x=affyIDVec[i], envir=get(paste(annot.pckg, "LOCUSID", sep = "")), mode = "any", ifnotfound = list(function(x) stop(paste("value for '", x, "' not found", sep = ""), call. = FALSE)), inherits = FALSE))} else {"-"} } #make LL vector unique and remove NA values x<-LocusLinkVec x<-as.numeric(unique(x)) o<-order(x) x<-x[o] ifis.na(x[length(x)])) {x<-x[1:(length(x) - 1)]} #Perform GoHyperG BP.hyperG<-GOHyperG(x, lib=annot.pckg, what="BP")

Thanks Jim. The problem probably exists in the soon to be released rgu34a 1.8.5 as well, as is tried both 1.8.4 and 1.8.5 with the same results. Mark Mark W. Kimpel MD -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Tuesday, September 20, 2005 8:12 AM To: Kimpel, Mark William Cc: Bioconductor Newsgroup Subject: Re: [BioC] GOstats error messages Kimpel, Mark William wrote: > I am still getting an Error Message when I use GOHyperG. The message > reads, "Error: value for 'L00981mRNA#2_at' not found". As you can see > from my script below, which replicates this error, that this Affy ID is > not on my original list. Please see my script below the sessionInfo to > replicate the error. Note that in my original post I mistakenly said > that I am using rat2302; I am actually using rgu34a. I believe this problem is due to the rgu34a 1.8.4 package, in particular the rgu34aGO2ALLPROBES environment: > as.list(rgu34aGO2ALLPROBES)[[1]][1:10] <na> IDA IEA IEA <na> "rc_AA924909_at" "S55427_s_at" "S55427_s_at" "AJ001320_at" "AJ011656cds_s_at" IDA IEA <na> IEA IEA "M74067_at" "M74067_at" "AJ011811_at" "AJ011811_g_at" "AB005549_at" None of these values is an Affymetrix ID - instead they appear to be a combination of a GenBank/RefSeq accession number and an Affy ID. Best, Jim > > Thanks, > > Mark > ###################################################################### ## > #### > My session info is: > > > R version 2.2.0, 2005-08-29, i386-pc-mingw32 > > attached base packages: > [1] "splines" "tools" "methods" "stats" "graphics" > "grDevices" "utils" "datasets" "base" > > other attached packages: > hgu95av2 GOstats genefilter xtable RBGL annotate > GO graph Ruuid cluster rgu34a limma rgu34acdf > multtest > "1.6.5" "1.2.0" "1.7.7" "1.2-5" "1.4.0" "1.6.3" > "1.6.5" "1.6.5" "1.6.2" "1.10.1" "1.8.5" "2.0.7" > "1.4.3" "1.7.3" > survival affy reposTools Biobase > "2.18" "1.7.2" "1.6.2" "1.7.0" > ###################################################################### ## > #### > > require(GOstats) > > affyIDVec<- c("AB000362_at", "AB000517_s_at", "AB001453_at", > "AB001576_s_at", "AB002086_at") > > annot.pckg<-"rgu34a" > > LocusLinkVec<-c(rep(NA,length(affyIDVec))) > > #map Affy IDs to Locus Link IDs > > for (i in 1:length(affyIDVec)) > > { > LocusLinkVec[i]<-if(!is.na(unlist(mget(x=affyIDVec[i], > envir=get(paste(annot.pckg, "LOCUSID", sep = "")), mode = "any", > ifnotfound = NA, inherits = > FALSE)))){unlist(mget(x=affyIDVec[i], envir=get(paste(annot.pckg, > "LOCUSID", sep = "")), mode = "any", > ifnotfound = list(function(x) stop(paste("value for '", > x, "' not found", sep = ""), call. = FALSE)), inherits = > FALSE))} else {"-"} > > } > > #make LL vector unique and remove NA values > > x<-LocusLinkVec > > x<-as.numeric(unique(x)) > > o<-order(x) > > x<-x[o] > > ifis.na(x[length(x)])) {x<-x[1:(length(x) - 1)]} > > #Perform GoHyperG > > BP.hyperG<-GOHyperG(x, lib=annot.pckg, what="BP") > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

The fix to rgu34a to make it compatible with GOstats resulted in no error messages this time around. Thanks so much for your very prompt attention and excellent help. Mark Mark W. Kimpel MD -----Original Message----- From: Ting-Yuan Liu (FHCRC) [mailto:tliu@fhcrc.org] Sent: Wednesday, September 21, 2005 2:01 AM To: Kimpel, Mark William Cc: James W. MacDonald; Bioconductor Newsgroup Subject: Re: [BioC] GOstats error messages Hi Mark, This problem is due to a bug in AnnBuilder. Simply speaking, AnnBuilder can not handle probeset ids with "#". This bug is fixed. The annotation packages in the coming release will not cause this kind of problem. Thanks for reporting this bug. Ting-Yuan On Tue, 20 Sep 2005, Kimpel, Mark William wrote: > Thanks Jim. The problem probably exists in the soon to be released > rgu34a 1.8.5 as well, as is tried both 1.8.4 and 1.8.5 with the same > results. > > Mark > > Mark W. Kimpel MD > > > > > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: Tuesday, September 20, 2005 8:12 AM > To: Kimpel, Mark William > Cc: Bioconductor Newsgroup > Subject: Re: [BioC] GOstats error messages > > Kimpel, Mark William wrote: > > I am still getting an Error Message when I use GOHyperG. The message > > reads, "Error: value for 'L00981mRNA#2_at' not found". As you can see > > from my script below, which replicates this error, that this Affy ID > is > > not on my original list. Please see my script below the sessionInfo to > > replicate the error. Note that in my original post I mistakenly said > > that I am using rat2302; I am actually using rgu34a. > > I believe this problem is due to the rgu34a 1.8.4 package, in particular > > the rgu34aGO2ALLPROBES environment: > > > as.list(rgu34aGO2ALLPROBES)[[1]][1:10] > <na> IDA IEA > IEA <na> > "rc_AA924909_at" "S55427_s_at" "S55427_s_at" > "AJ001320_at" "AJ011656cds_s_at" > IDA IEA <na> > IEA IEA > "M74067_at" "M74067_at" "AJ011811_at" > "AJ011811_g_at" "AB005549_at" > > > None of these values is an Affymetrix ID - instead they appear to be a > combination of a GenBank/RefSeq accession number and an Affy ID. > > Best, > > Jim > > > > > > > Thanks, > > > > Mark > > > ###################################################################### ## > > #### > > My session info is: > > > > > > R version 2.2.0, 2005-08-29, i386-pc-mingw32 > > > > attached base packages: > > [1] "splines" "tools" "methods" "stats" "graphics" > > "grDevices" "utils" "datasets" "base" > > > > other attached packages: > > hgu95av2 GOstats genefilter xtable RBGL annotate > > GO graph Ruuid cluster rgu34a limma rgu34acdf > > multtest > > "1.6.5" "1.2.0" "1.7.7" "1.2-5" "1.4.0" "1.6.3" > > "1.6.5" "1.6.5" "1.6.2" "1.10.1" "1.8.5" "2.0.7" > > "1.4.3" "1.7.3" > > survival affy reposTools Biobase > > "2.18" "1.7.2" "1.6.2" "1.7.0" > > > ###################################################################### ## > > #### > > > > require(GOstats) > > > > affyIDVec<- c("AB000362_at", "AB000517_s_at", "AB001453_at", > > "AB001576_s_at", "AB002086_at") > > > > annot.pckg<-"rgu34a" > > > > LocusLinkVec<-c(rep(NA,length(affyIDVec))) > > > > #map Affy IDs to Locus Link IDs > > > > for (i in 1:length(affyIDVec)) > > > > { > > LocusLinkVec[i]<-if(!is.na(unlist(mget(x=affyIDVec[i], > > envir=get(paste(annot.pckg, "LOCUSID", sep = "")), mode = "any", > > ifnotfound = NA, inherits = > > FALSE)))){unlist(mget(x=affyIDVec[i], envir=get(paste(annot.pckg, > > "LOCUSID", sep = "")), mode = "any", > > ifnotfound = list(function(x) stop(paste("value for '", > > x, "' not found", sep = ""), call. = FALSE)), inherits = > > FALSE))} else {"-"} > > > > } > > > > #make LL vector unique and remove NA values > > > > x<-LocusLinkVec > > > > x<-as.numeric(unique(x)) > > > > o<-order(x) > > > > x<-x[o] > > > > ifis.na(x[length(x)])) {x<-x[1:(length(x) - 1)]} > > > > #Perform GoHyperG > > > > BP.hyperG<-GOHyperG(x, lib=annot.pckg, what="BP") > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >