Bioconductors- I have produced the following error upon calling hyperGTest with several different datasets. I have reproduced the error below using data from the ALL set and code parsed from the GOStats vignette. Any help would be appreciated. Cheers, -Casey > data(ALL, package = "ALL") > Bcell <- grep("^B", as.character(ALL$BT)) > subsetType <- "ALL/AF4" > bcrAblOrNegIdx <- which(as.character(ALL$mol) %in% c("NEG", subsetType)) > bcrAblOrNeg <- ALL[, intersect(Bcell, bcrAblOrNegIdx)] > bcrAblOrNeg$mol.biol = factor(bcrAblOrNeg$mol.biol) > > entrezIds <- mget(featureNames(bcrAblOrNeg), envir = hgu95av2ENTREZID) > haveEntrezId <- names(entrezIds)[sapply(entrezIds, function(x) ! is.na(x))] > bcrAblOrNeg <- bcrAblOrNeg[haveEntrezId, ] > haveGo <- sapply(mget(featureNames(bcrAblOrNeg), hgu95av2GO), + function(x) { if (length(x) == 1 && is.na(x)) FALSE else TRUE }) > bcrAblOrNeg <- bcrAblOrNeg[haveGo, ] > > iqrCutoff <- 0.5 > bcrAblOrNegIqr <- apply(exprs(bcrAblOrNeg), 1, IQR) > selected <- bcrAblOrNegIqr > iqrCutoff > > nsFiltered <- bcrAblOrNeg[selected, ] > nsFilteredIqr <- bcrAblOrNegIqr[selected] > uniqGenes <- findLargest(featureNames(nsFiltered), nsFilteredIqr, + "hgu95av2") > nsFiltered <- nsFiltered[uniqGenes, ] > > ttestCutoff <- 0.05 > ttests = rowttests(nsFiltered, "mol.biol") > smPV = ttests$p.value < ttestCutoff > pvalFiltered <- nsFiltered[smPV, ] > selectedEntrezIds <- unlist(mget(featureNames(pvalFiltered), + hgu95av2ENTREZID)) > > hgCutoff <- 0.001 > params <- new("GOHyperGParams", geneIds = selectedEntrezIds, annotation = "hgu95av2.db", + ontology = "BP", pvalueCutoff = hgCutoff, conditional = FALSE, + testDirection = "over") > > hgOver <- hyperGTest(params) Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: cannot join using column _id - column not present in both tables) > traceback() 13: .Call("RS_SQLite_exec", conId, statement, bind.data, PACKAGE = .SQLitePkgName) 12: sqliteExecStatement(con, statement, bind.data) 11: sqliteQuickSQL(conn, statement, ...) 10: dbGetQuery(db, SQL) 9: dbGetQuery(db, SQL) 8: getGoToEntrezMap_db(p) 7: categoryToEntrezBuilder(p) 6: categoryToEntrezBuilder(p) 5: .class1(object) 4: .class1(object) 3: is(object, Cl) 2: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", "hyperGTest") 1: hyperGTest(params) > sessionInfo() R version 2.6.2 (2008-02-08) i386-apple-darwin8.10.1 locale: en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] RColorBrewer_1.0-2 GOstats_2.4.0 Category_2.6.0 RBGL_1.14.0 graph_1.18.0 [6] genefilter_1.16.0 survival_2.34 annotate_1.16.1 xtable_1.5-2 GO.db_2.0.2 [11] hgu95av2.db_2.0.2 AnnotationDbi_1.0.6 RSQLite_0.6-8 DBI_0.2-4 ALL_1.4.3 [16] Biobase_1.16.3 loaded via a namespace (and not attached): [1] cluster_1.11.9 ------------------------ Christopher Brown Institute for Genomics and Systems Biology University of Chicago CLSC Room 431 920 E. 58th. St. Chicago, IL, 60637 Lab: (773) 834-0074 caseybrown [at] uchicago.edu [[alternative HTML version deleted]]

Hi Christopher, Thanks for the report. Part of the reason to ask for a self-contained example is that there is some chance that you have personally actually run it, and part of the reason is to make it easy for me (or someone who might want to help) to cut and paste from your email. Your example fails on both counts. I have to edit out the > and other bits that you cut from your R session before I can run it, and this script doesn't run, as all calls to library are missing Adding these to the start: library(ALL) library(hgu95av2.db) library(genefilter) library(GOstats) yields something that runs just fine in the current release, so I can only suggest that you update your R, and bioc appropriately and you should have no problems. Part of your problem may also stem from the fact that you are doing exactly what we advise against, and that is mixing and matching different versions of packages inappropriately. Please use biocLite - it is intended to keep you from having these sorts of problems. best wishes Robert other attached packages: [1] GOstats_2.6.0 Category_2.6.0 RBGL_1.16.0 [4] annotate_1.18.0 xtable_1.5-2 GO.db_2.2.0 [7] graph_1.18.0 genefilter_1.20.0 survival_2.34-1 [10] hgu95av2.db_2.2.0 AnnotationDbi_1.2.0 RSQLite_0.6-8 [13] DBI_0.2-4 ALL_1.4.3 Biobase_2.0.0 Christopher Brown wrote: > Bioconductors- > I have produced the following error upon calling hyperGTest with > several different datasets. I have reproduced the error below using > data from the ALL set and code parsed from the GOStats vignette. Any > help would be appreciated. Cheers, > > -Casey > > > data(ALL, package = "ALL") > > Bcell <- grep("^B", as.character(ALL$BT)) > > subsetType <- "ALL/AF4" > > bcrAblOrNegIdx <- which(as.character(ALL$mol) %in% c("NEG", > subsetType)) > > bcrAblOrNeg <- ALL[, intersect(Bcell, bcrAblOrNegIdx)] > > bcrAblOrNeg$mol.biol = factor(bcrAblOrNeg$mol.biol) > > > > entrezIds <- mget(featureNames(bcrAblOrNeg), envir = > hgu95av2ENTREZID) > > haveEntrezId <- names(entrezIds)[sapply(entrezIds, function(x) ! > is.na(x))] > > bcrAblOrNeg <- bcrAblOrNeg[haveEntrezId, ] > > haveGo <- sapply(mget(featureNames(bcrAblOrNeg), hgu95av2GO), > + function(x) { if (length(x) == 1 && is.na(x)) FALSE else TRUE }) > > bcrAblOrNeg <- bcrAblOrNeg[haveGo, ] > > > > iqrCutoff <- 0.5 > > bcrAblOrNegIqr <- apply(exprs(bcrAblOrNeg), 1, IQR) > > selected <- bcrAblOrNegIqr > iqrCutoff > > > > nsFiltered <- bcrAblOrNeg[selected, ] > > nsFilteredIqr <- bcrAblOrNegIqr[selected] > > uniqGenes <- findLargest(featureNames(nsFiltered), nsFilteredIqr, > + "hgu95av2") > > nsFiltered <- nsFiltered[uniqGenes, ] > > > > ttestCutoff <- 0.05 > > ttests = rowttests(nsFiltered, "mol.biol") > > smPV = ttests$p.value < ttestCutoff > > pvalFiltered <- nsFiltered[smPV, ] > > selectedEntrezIds <- unlist(mget(featureNames(pvalFiltered), > + hgu95av2ENTREZID)) > > > > hgCutoff <- 0.001 > > params <- new("GOHyperGParams", geneIds = selectedEntrezIds, > annotation = "hgu95av2.db", > + ontology = "BP", pvalueCutoff = hgCutoff, conditional = FALSE, > + testDirection = "over") > > > > hgOver <- hyperGTest(params) > Error in sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (error in statement: cannot join using column _id - > column not present in both tables) > > > traceback() > 13: .Call("RS_SQLite_exec", conId, statement, bind.data, PACKAGE > = .SQLitePkgName) > 12: sqliteExecStatement(con, statement, bind.data) > 11: sqliteQuickSQL(conn, statement, ...) > 10: dbGetQuery(db, SQL) > 9: dbGetQuery(db, SQL) > 8: getGoToEntrezMap_db(p) > 7: categoryToEntrezBuilder(p) > 6: categoryToEntrezBuilder(p) > 5: .class1(object) > 4: .class1(object) > 3: is(object, Cl) > 2: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", > "hyperGTest") > 1: hyperGTest(params) > > > sessionInfo() > R version 2.6.2 (2008-02-08) > i386-apple-darwin8.10.1 > > locale: > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] RColorBrewer_1.0-2 GOstats_2.4.0 Category_2.6.0 > RBGL_1.14.0 graph_1.18.0 > [6] genefilter_1.16.0 survival_2.34 annotate_1.16.1 > xtable_1.5-2 GO.db_2.0.2 > [11] hgu95av2.db_2.0.2 AnnotationDbi_1.0.6 RSQLite_0.6-8 > DBI_0.2-4 ALL_1.4.3 > [16] Biobase_1.16.3 > > loaded via a namespace (and not attached): > [1] cluster_1.11.9 > > > > > > ------------------------ > Christopher Brown > Institute for Genomics and Systems Biology > University of Chicago > CLSC Room 431 > 920 E. 58th. St. > Chicago, IL, 60637 > Lab: (773) 834-0074 > caseybrown [at] uchicago.edu > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > -- 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