Thanks. I thought about it, but I did not find the 'E' in this example from GO website: http://www.geneontology.org/GO.evidence.shtml Another question is for GOstats: is the evidence code involved in the enrichment analysis? ======================= Here I repeat part of the annotation that I got: ENTREZID PROBE ACCNUM UNIGENE [1,] "10" "36512_at" "L32179" "Hs.2" [2,] "10" "38912_at" "D90042" "Hs.2" [3,] "1084" "32468_f_at" "D90278;M16652" "NA" [4,] "125" "35730_at" "X03350" "NA" [5,] "2" "32469_at" "L00693" "Hs.74561" [6,] "63036" "38936_at" "M16652" "NA" [7,] "7051" "32481_at" "AL031663" "NA" [8,] "9" "33825_at" "X68733" "NA" [9,] "NA" "39368_at" "AL031668" "NA" GO OMIM [1,] "GO:0004060 at E" "NA" [2,] "GO:0004060 at E" "NA" [3,] "NA" "NA" [4,] "NA" "NA" [5,] "GO:0008320 at NR;GO:0004866 at NR;GO:0006886 at NR" "NA" [6,] "NA" "NA" [7,] "NA" "NA" [8,] "GO:0004060 at E" "NA" [9,] "NA" "NA" ======================= Here is the script that I used while following the example: library(AnnBuilder); pkgpath <- .find.package("AnnBuilder"); # test dataset pkgdir <- "/nethome/xpeng/linux/analysis/array/scripts/pkgs"; setwd(pkgdir); geneNMap <- matrix(c("32468_f_at", "D90278;M16652", "32469_at", "L00693", "32481_at", "AL031663", "33825_at", "X68733", "35730_at", "X03350", "36512_at", "L32179", "38912_at", "D90042", "38936_at", "M16652", "39368_at", "AL031668"), ncol = 2, byrow = TRUE) write.table(geneNMap, file = "geneNMap", sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE) # get annotation info. makeSrcInfo() srcObjs <- list() egUrl <- "http://www.bioconductor.org/datafiles/wwwsources" ugUrl <- "http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz" eg <- EG(srcUrl = egUrl, parser = file.path(pkgpath, "scripts", "gbLLParser"), baseFile = "geneNMap", accession = "Tll_tmpl.gz", built = "N/A", fromWeb = TRUE) ug <- UG(srcUrl = ugUrl, parser = file.path(pkgpath, "scripts", "gbUGParser"), baseFile = "geneNMap", organism = "Homo sapiens", built = "N/A", fromWeb = TRUE) srcObjs[["eg"]] <- eg srcObjs[["ug"]] <- ug if(.Platform$OS.type != "windows"){ llMapping <- parseData(eg, eg at accession) colnames(llMapping) <- c("PROBE", "EG") ugMapping <- parseData(ug) colnames(ugMapping) <- c("PROBE", "UG") } # This portion only runs after the previous code has been # executed under windows if(.Platform$OS.type != "windows"){ llMapping ugMapping } # This portion only runs interactively under Windows (copy/paste) base <- matrix(scan("geneNMap", what = "", sep = "\t", quote = "", quiet = TRUE), ncol = 2, byrow = TRUE) colnames(base) <- c("PROBE", "ACC") merged <- merge(base, llMapping, by = "PROBE", all.x = TRUE) merged <- merge(merged, ugMapping, by = "PROBE", all.x = TRUE) unified <- AnnBuilder:::resolveMaps(merged, trusted = c("EG", "UG"), srcs = c("EG", "UG")) unified read.table(unified, sep = "\t", header = FALSE) if(.Platform$OS.type != "windows"){ # these two do not work for me # parser(eg) <- file.path(.path.package("AnnBuilder"), "scripts", "llParser") # baseFile(eg) <- unified attr(eg, "parser") <- file.path(.path.package("AnnBuilder"), "scripts", "llParser") attr(eg, "baseFile") <- unified annotation <- parseData(eg, eg at accession, ncol = 14) colnames(annotation) <- c("PROBE", "ACCNUM", "ENTREZID", "UNIGENE", "GENENAME", "SYMBOL","CHR", "MAP", "PMID", "GRIF", "SUMFUNC", "GO", "OMIM", "REFSEQ") } annotation gpUrl <- "http://www.bioconductor.org/datafiles/wwwsources/" goUrl <- "http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml" gp <- GP(srcUrl = gpUrl, organism = "Homo sapiens", fromWeb = TRUE) go <- GO(srcUrl = goUrl, fromWeb = TRUE) strand <- AnnBuilder:::getChroLocation(srcUrl(gp), AnnBuilder:::gpLinkNGene(TRUE)); strand annotation <- merge(annotation, strand, by = "ENTREZID", all.x = TRUE); pkgName <- "myTestPkg" pkgPath <- getwd() createEmptyDPkg("myTestPkg", getwd(), force = TRUE) annotation <- as.matrix(annotation) annotation AnnBuilder:::writeAnnData2Pkg(annotation, pkgName, pkgPath) list.files(file.path(getwd(), "myTestPkg")) repList <- AnnBuilder:::getRepList("all", srcObjs) repList[["PKGNAME"]] <- pkgName AnnBuilder:::writeOrganism(pkgName, pkgPath, "Homo sapiens") AnnBuilder:::writeDocs("geneNMap", pkgName, pkgPath, "1.1.0", list(author = "annonymous", maintainer = "annonymous <annonymous at="" net.com="">"), repList, "PKGNAME") # clean up #unlink(c(unified, XMLOut, "geneNMap", "test.xml", "testByNum.xml")) #unlink(file.path(getwd(), "test"), TRUE) sessionInfo() ======================= This is the session info: R version 2.5.0 (2007-04-23) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .U TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UT F- 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ ID ENTIFICATION=C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: AnnBuilder annotate XML Biobase "1.14.0" "1.14.1" "1.7-3" "1.14.0" Best, Xinxia -----Original Message----- From: John Zhang [mailto:jzhang@jimmy.harvard.edu] Sent: Tuesday, May 01, 2007 5:51 AM To: bioconductor at stat.math.ethz.ch; Xinxia Peng Subject: Re: [BioC] AnnBuilder with custmerized GO annotation > >What do these after a GO term mean, '@E' or '@NR'? They are evidence code by GO. Please read the description available from GO web site for details. > >What I am trying to do is to build an annotation package for GO >enrichment analysis using GOstats. The GO annotation is from >InterProScan. I plan to create a data frame with three columns: probeid, >geneid and GO, then build the annotation package. Any suggestions? > >Thanks, >Xinxia > >_______________________________________________ >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 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

In the particular example, the corresponding protein on GO website is 'ARY2_HUMAN'. It has one associated GO term GO:0004060, the same one as I got from the example. But the evidence code is 'TAS'. I am wondering if it is related to the data stored on the bioconductor site, or something happened along the file parsing or something else. Xinxia -----Original Message----- From: Seth Falcon [mailto:sfalcon@fhcrc.org] Sent: Tuesday, May 01, 2007 12:10 PM To: Xinxia Peng Cc: John Zhang; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] AnnBuilder with custmerized GO annotation "Xinxia Peng" <xinxia.peng at="" sbri.org=""> writes: > Thanks. I thought about it, but I did not find the 'E' in this example > from GO website: That looks like a bug of some sort. The evidence codes should all be three letters I believe. > http://www.geneontology.org/GO.evidence.shtml > > Another question is for GOstats: is the evidence code involved in the > enrichment analysis? No, they are not used at present. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org