I wonder if somebody can tell me how I can use my P values from the limma test as input into topGo. This is what I tried: In topGo I usually do the following using the standard t-test: > geneList <- getPvalues(exprs(esetSub), classlabel = y, alternative = "two.sided", correction = "BH") > geneList[1:10] 1415670_at 1415671_at 1415672_at 1415673_at 1415674_a_at 1415675_at 0.15021513 0.07711458 0.38562825 0.78996178 0.64844312 0.16257882 1415676_a_at 1415677_at 1415678_at 1415679_at 0.92404052 0.01690829 0.30654309 0.55264382 > length(geneList) [1] 9103 > topDiffGenes <- function(allScore) { + return(allScore < 0.01) + } > GOdata <- new("topGOdata", + ontology = "BP", + allGenes = geneList, + geneSel = topDiffGenes, + description = "GO analysis of data. Diff. Expre. between WT and IL10", + annot = annFUN.hgu, + affyLib = affyLib) Building most specific GOs ..... ( 2088 GO terms found. ) Build GO DAG topology .......... ( 3286 GO terms and 5438 relations. ) Annotating nodes ............... ( 6088 genes annotated to the GO terms. ) I tried to replace geneList with the results from limma in the following way: > geneList<-as.array(mytable$P.Value) > dimnames(geneList) <- list(mytable$ID) This gives me a genelist just as the one before except that the results are ordered by P-value as they come from the limma table > geneList[1:10] 1423677_at NuGO_emt025263_at 1421628_at 1436576_at 4.335431e-10 2.530289e-09 4.326564e-09 4.470340e-09 1450034_at 1422632_at 1453080_at 1438037_at 5.625014e-09 5.931422e-09 6.114187e-09 6.872450e-09 1422953_at 1446280_at 1.078998e-08 1.143128e-08 > length(geneList) [1] 9103 but when I use this as input in topGo I get an error message: > topDiffGenes <- function(allScore) { + return(allScore < 0.01) + } > GOdata <- new("topGOdata", + ontology = "BP", + allGenes = geneList, + geneSel = topDiffGenes, + description = "WT versus Il10 ko", + annot = annFUN.hgu, + affyLib = affyLib) Error in checkSlotAssignment(object, name, value) : assignment of an object of class "AsIs" is not valid for slot "allGenes" in an object of class "topGOdata"; is(value, "character") is not TRUE > Hope somebody can help, Many thanks Caroline

Hi Caroline, You need an as.character() for the gene names. So you might need to construct your genelist differently. Something like genelist <- mytable$P.Value names(genelist) <- as.character(mytable[,1]) should work. Best, Jim Caroline Reiff wrote: > I wonder if somebody can tell me how I can use my P values from the limma > test as input into topGo. This is what I tried: > In topGo I usually do the following using the standard t-test: > > geneList <- getPvalues(exprs(esetSub), classlabel = y, alternative = > "two.sided", correction = "BH") > > geneList[1:10] > 1415670_at 1415671_at 1415672_at 1415673_at 1415674_a_at > 1415675_at > 0.15021513 0.07711458 0.38562825 0.78996178 0.64844312 > 0.16257882 > 1415676_a_at 1415677_at 1415678_at 1415679_at > 0.92404052 0.01690829 0.30654309 0.55264382 > > length(geneList) > [1] 9103 > > topDiffGenes <- function(allScore) { > + return(allScore < 0.01) > + } > > GOdata <- new("topGOdata", > + ontology = "BP", > + allGenes = geneList, > + geneSel = topDiffGenes, > + description = "GO analysis of data. Diff. Expre. between WT and IL10", > + annot = annFUN.hgu, > + affyLib = affyLib) > Building most specific GOs ..... ( 2088 GO terms found. ) > Build GO DAG topology .......... ( 3286 GO terms and 5438 relations. > ) > Annotating nodes ............... ( 6088 genes annotated to the GO > terms. ) > I tried to replace geneList with the results from limma in the following > way: > > geneList<-as.array(mytable$P.Value) > > dimnames(geneList) <- list(mytable$ID) > This gives me a genelist just as the one before except that the results are > ordered by P-value as they come from the limma table > > geneList[1:10] > 1423677_at NuGO_emt025263_at 1421628_at 1436576_at > 4.335431e-10 2.530289e-09 4.326564e-09 4.470340e-09 > 1450034_at 1422632_at 1453080_at 1438037_at > 5.625014e-09 5.931422e-09 6.114187e-09 6.872450e-09 > 1422953_at 1446280_at > 1.078998e-08 1.143128e-08 > > length(geneList) > [1] 9103 > but when I use this as input in topGo I get an error message: > > topDiffGenes <- function(allScore) { > + return(allScore < 0.01) > + } > > GOdata <- new("topGOdata", > + ontology = "BP", > + allGenes = geneList, > + geneSel = topDiffGenes, > + description = "WT versus Il10 ko", > + annot = annFUN.hgu, > + affyLib = affyLib) > Error in checkSlotAssignment(object, name, value) : > assignment of an object of class "AsIs" is not valid for slot > "allGenes" in an object of class "topGOdata"; is(value, "character") is not > TRUE > > > Hope somebody can help, Many thanks Caroline > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

Hi Caroline, you are using the "array" type for the geneList. topGO expects a "character vector" instead. It is a good practice to use the str() function to see which type of data are you using and if you need any coercion. Let me give you an example: ## build a 1-dim array (of type character) > x <- as.array(letters[1:10]) > dimnames(x) <- list(LETTERS[1:10]) ## you can see the structure: > str(x) chr [, 1:10] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" - attr(*, "dimnames")=List of 1 ..$ : chr [1:10] "A" "B" "C" "D" ... ## build a character vector > y <- as.character(letters[1:10]) > names(y) <- as.character(LETTERS[1:10]) > str(y) Named chr [1:10] "a" "b" "c" "d" "e" "f" "g" "h" "i" ... - attr(*, "names")= chr [1:10] "A" "B" "C" "D" ... ################### As you see x differ in structure from y. Thus what you need to do is the following: > geneList<-as.character(mytable$P.Value) > names(geneList) <- as.character(mytable$ID) Hope this helps, Adrian On 11/8/07, Caroline Reiff <c.reiff at="" rri.sari.ac.uk=""> wrote: > > I wonder if somebody can tell me how I can use my P values from the limma > test as input into topGo. This is what I tried: > In topGo I usually do the following using the standard t-test: > > geneList <- getPvalues(exprs(esetSub), classlabel = y, alternative = > "two.sided", correction = "BH") > > geneList[1:10] > 1415670_at 1415671_at 1415672_at 1415673_at 1415674_a_at > 1415675_at > 0.15021513 0.07711458 0.38562825 0.78996178 0.64844312 > 0.16257882 > 1415676_a_at 1415677_at 1415678_at 1415679_at > 0.92404052 0.01690829 0.30654309 0.55264382 > > length(geneList) > [1] 9103 > > topDiffGenes <- function(allScore) { > + return(allScore < 0.01) > + } > > GOdata <- new("topGOdata", > + ontology = "BP", > + allGenes = geneList, > + geneSel = topDiffGenes, > + description = "GO analysis of data. Diff. Expre. between WT and IL10", > + annot = annFUN.hgu, > + affyLib = affyLib) > Building most specific GOs ..... ( 2088 GO terms found. ) > Build GO DAG topology .......... ( 3286 GO terms and 5438 relations. > ) > Annotating nodes ............... ( 6088 genes annotated to the GO > terms. ) > I tried to replace geneList with the results from limma in the following > way: > > geneList<-as.array(mytable$P.Value) > > dimnames(geneList) <- list(mytable$ID) > This gives me a genelist just as the one before except that the results are > ordered by P-value as they come from the limma table > > geneList[1:10] > 1423677_at NuGO_emt025263_at 1421628_at 1436576_at > 4.335431e-10 2.530289e-09 4.326564e-09 4.470340e-09 > 1450034_at 1422632_at 1453080_at 1438037_at > 5.625014e-09 5.931422e-09 6.114187e-09 6.872450e-09 > 1422953_at 1446280_at > 1.078998e-08 1.143128e-08 > > length(geneList) > [1] 9103 > but when I use this as input in topGo I get an error message: > > topDiffGenes <- function(allScore) { > + return(allScore < 0.01) > + } > > GOdata <- new("topGOdata", > + ontology = "BP", > + allGenes = geneList, > + geneSel = topDiffGenes, > + description = "WT versus Il10 ko", > + annot = annFUN.hgu, > + affyLib = affyLib) > Error in checkSlotAssignment(object, name, value) : > assignment of an object of class "AsIs" is not valid for slot > "allGenes" in an object of class "topGOdata"; is(value, "character") is not > TRUE > > > Hope somebody can help, Many thanks Caroline > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >