Question: GO-Analysis using TopGO for Yeast2 data
0
gravatar for Tobias Koschubs
11.6 years ago by
Tobias Koschubs10 wrote:
Hi! I tried to do a GO-Analysis using the TopGO package with Affymetrix Yeast2 Expression data but encountered a couple of problems. As I'm new to Bioconductor, I would be very grateful to get some help. The Yeast2-Package related problems are the following: Very recently, the GO-Annotations have been updated and now include also the annotations from computationally predicted methods (available from yeastgenome.org and geneontology.org). Of course, I would like to use the newest annotations and I tried to use the AnnBuilder yeastPkgBuilder-method. However, I didn't succeed to bring the gene_association.sgd file together with the Probe mappings on the chip. I guess one would need to use the ORFs as identifiers instead of the SGD-identifiers from the gene_association file. Moreover, I didn't figure out how to set the path for the annotation file as local (it was suggested to unpack it in advance). Is there someone from the Biocore Data Team who has the proper scripts to do it? With the TopGO package, I did the GO Analysis using the current yeast2 annotations. Unfortunately, it's documentation lacks some details and I didn't figure out, how to print out the genes (or at least the probes) according to the top-GO-terms listed by the genTable-Method. From the source-code, I learned that there's a printGenes-method which possible should do this. However, the yeast2 chip is a bit different from others as it doesn't use ENTREZIDs or SYMBOLS and I also didn't figure out what are the parameters of this method. Best and thanks in advance, Tobias Koschubs
annotation go yeast2 probe topgo • 1.1k views
ADD COMMENTlink modified 11.6 years ago by Marc Carlson7.2k • written 11.6 years ago by Tobias Koschubs10
Answer: GO-Analysis using TopGO for Yeast2 data
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gravatar for Marc Carlson
11.6 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Tobias Koschubs wrote: > Hi! > > I tried to do a GO-Analysis using the TopGO package with Affymetrix > Yeast2 Expression data but encountered a couple of problems. As I'm new > to Bioconductor, I would be very grateful to get some help. > > The Yeast2-Package related problems are the following: Very recently, > the GO-Annotations have been updated and now include also the > annotations from computationally predicted methods (available from > yeastgenome.org and geneontology.org). Of course, I would like to use > the newest annotations and I tried to use the AnnBuilder > yeastPkgBuilder-method. However, I didn't succeed to bring the > gene_association.sgd file together with the Probe mappings on the chip. > I guess one would need to use the ORFs as identifiers instead of the > SGD-identifiers from the gene_association file. Moreover, I didn't > figure out how to set the path for the annotation file as local (it was > suggested to unpack it in advance). Is there someone from the Biocore > Data Team who has the proper scripts to do it? > > With the TopGO package, I did the GO Analysis using the current yeast2 > annotations. Unfortunately, it's documentation lacks some details and I > didn't figure out, how to print out the genes (or at least the probes) > according to the top-GO-terms listed by the genTable-Method. From the > source-code, I learned that there's a printGenes-method which possible > should do this. However, the yeast2 chip is a bit different from others > as it doesn't use ENTREZIDs or SYMBOLS and I also didn't figure out what > are the parameters of this method. > > Best and thanks in advance, > Tobias Koschubs > > _______________________________________________ > 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 > > It's hard to help you because we don't have the results of your sessionInfo() or the code you were trying to run. You might want to look here for some helpful tips on how to ask questions of the boards: http://www.bioconductor.org/docs/postingGuide.html So presently, I am just not sure if this is what you need or not, but I will make a guess and tell you that if you want to get the usual gene symbols from the yeast2 package, you should be looking at the yeast2GENENAME map. Marc
ADD COMMENTlink written 11.6 years ago by Marc Carlson7.2k
Answer: GO-Analysis using TopGO for Yeast2 data
0
gravatar for Adrian Alexa
11.6 years ago by
Adrian Alexa400
Adrian Alexa400 wrote:
Hi Tobias, you are right about the issues with the topGO. The printGenes() function won't work with the yeast2 package. Bellow is a simple session in which a performed a dummy enrichment analysis for the using the yeas2 annotations. You will find a copy of the printGenes() function which will work with the yeast2 library. You can also add more information into the table if you want with minimal code chnages. I will try to document better this function (and many others) in the next release of the Bioconductor. As well, there will be a more comprehensive vignette. It will be hard to have a function with the same name that will work on yeast2 and other Affy libraries, given the structural difference. However I put it on my TODO list and I'll see what I can come up with. Thanks for bringing this up. Let me know if you have more questions, Adrian ---------------------------------------------------------- library(topGO) ## get the library affyLib <- "yeast2" library(package = affyLib, character.only = TRUE) geneNames <- ls(yeast2GO) myInterestedGenes <- sample(geneNames, 500) geneList <- factor(as.integer(geneNames %in% myInterestedGenes)) names(geneList) <- geneNames ## build the topGOdata class GOyeast2 <- new("topGOdata", ontology = "BP", allGenes = geneList, description = "stability of GO - ALL dataset.", nodeSize = 5, annot = annFUN.hgu, affyLib = affyLib) result <- runTest(GOyeast2, "classic", "fisher") tableFis <- GenTable(GOyeast2, pValue = result, topNodes = 10, numChar = 40) printGenesY <- function(object, whichTerms, affyLib, numChar = 100, simplify = TRUE, geneCufOff = 50, pvalCutOff) { term.genes <- genesInTerm(object, whichTerms) all.genes <- character() lapply(term.genes, function(x) all.genes <<- union(x, all.genes)) ORF.lib <- get(paste(affyLib, "ORF", sep = "")) CHR.lib <- get(paste(affyLib, "CHR", sep = "")) GNAME.lib <- get(paste(affyLib, "GENENAME", sep = "")) probeMapping <- data.frameORF.id = unlist(mget(all.genes, envir = ORF.lib, ifnotfound = NA)), CHR = as.integer(unlist(mget(all.genes, envir = CHR.lib, ifnotfound = NA)))) retList <- vector("list", length(whichTerms)) names(retList) <- whichTerms for(gt in whichTerms) { affID <- term.genes[[gt]] pval <- sort(geneScore(object, affID, use.names = TRUE)) if(missing(pvalCutOff)) affID <- names(pval) else { pval <- pval[pval <= pvalCutOff] affID <- names(pval) } ## we restrict the output to the number of genes length(affID) <- min(length(affID), geneCufOff) ## if there are no genes, there is nothing to print if(length(affID) == 0) { cat("\n\t No genes over the cutOff for:", gt, "\n") next } genesNames <- sapply(mget(affID, envir = GNAME.lib), function(x) return(x[1])) genesNames <- paste(substr(genesNames, 1, numChar), ifelse(nchar(genesNames) > numChar, "...", ""), sep = "") retList[[gt]] <- cbind("Affy ID" = affID, probeMapping[affID, ], "Gene name" = genesNames, "raw p-value" = format.pval(pval[affID], dig = 3, eps = 1e-30)) } ## if we have only one GO term we return just the data.frame if(simplify && length(whichTerms) == 1) return(retList[[1]]) return(retList) } selGOterms <- tableFis$GO.ID gg <- printGenesY(GOyeast2, whichTerms = selGOterms, affyLib = affyLib, numChar = 50) library(xtable) index <- order(sapply(gg, nrow)) for(g in names(gg)[index]) { curTab <- apply(gg[[g]], 2, function(x) {return(gsub("_", ".", as.character(x)))}) cat("\\begin{table}[bth]\n \\centering\\resizebox{.99\\linewidth}{!}{%\n") print(xtable(curTab), floating = FALSE) cat("}\\caption{", g, "}\n\\end{table}\n\n") } ---------------------------------------------------------------------- --------------------------------------------------------------------- On Tue, Mar 25, 2008 at 8:32 AM, Tobias Koschubs <biotekk2000 at="" compuserve.de=""> wrote: > Hi! > > I tried to do a GO-Analysis using the TopGO package with Affymetrix > Yeast2 Expression data but encountered a couple of problems. As I'm new > to Bioconductor, I would be very grateful to get some help. > > The Yeast2-Package related problems are the following: Very recently, > the GO-Annotations have been updated and now include also the > annotations from computationally predicted methods (available from > yeastgenome.org and geneontology.org). Of course, I would like to use > the newest annotations and I tried to use the AnnBuilder > yeastPkgBuilder-method. However, I didn't succeed to bring the > gene_association.sgd file together with the Probe mappings on the chip. > I guess one would need to use the ORFs as identifiers instead of the > SGD-identifiers from the gene_association file. Moreover, I didn't > figure out how to set the path for the annotation file as local (it was > suggested to unpack it in advance). Is there someone from the Biocore > Data Team who has the proper scripts to do it? > > With the TopGO package, I did the GO Analysis using the current yeast2 > annotations. Unfortunately, it's documentation lacks some details and I > didn't figure out, how to print out the genes (or at least the probes) > according to the top-GO-terms listed by the genTable-Method. From the > source-code, I learned that there's a printGenes-method which possible > should do this. However, the yeast2 chip is a bit different from others > as it doesn't use ENTREZIDs or SYMBOLS and I also didn't figure out what > are the parameters of this method. > > Best and thanks in advance, > Tobias Koschubs > > _______________________________________________ > 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 >
ADD COMMENTlink written 11.6 years ago by Adrian Alexa400
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