Seth and Jenny, I had the exact same problem last night using code of mine that had been working the past year. I updated all packages and the problem persisted. I would have reported it but was too busy with something that was due today. I am also using R-devel. Mark --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** Seth Falcon wrote: > Hi Jenny, > > Jenny Drnevich <drnevich at="" uiuc.edu=""> writes: >> Hi Seth and everyone, >> >> First, we will all miss you Seth! Good luck in your new career. But >> while you're still with Bioconductor, hopefully you can help me with a >> problem I'm having with GOstats in R-devel 2.6. I'm copying and >> pasting directly from the vignette GOstatsHyperG.pdf, Aug 23, 2007, >> and everything's fine until this point: >> >>> hgOver <- hyperGTest(params) >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "edges", for >> signature "graphNEL" >> >> (sessionInfo below) > > You have an old version of AnnotationDbi, can you try updating and > seeing if that fixes things? You might want to do an update of all of > your packages: > > library("Biobase") > update.packages(repos=biocReposList()) > > + seth > >

Hi Seth & Mark, After updating all packages, it does work (see long code and sessionInfo() below). However, are you using a different version of the vignette than the one I get from GOstats 2.3.16, dated Aug 30, 2007? If so, then I'm surprised it built because it's missing a line of code to create the subsetType object used in the first chuck of code after loading all the libraries. I highlighted this part in the code below. I only knew how to fix it because I had your GOstats handout from the BioC2007 workshop, which does have the correct code. Thanks, Jenny R version 2.6.0 Under development (unstable) (2007-08-28 r42679) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > update.packages(ask='graphics') --- Please select a CRAN mirror for use in this session --- trying URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.6/RSQLite_0. 6-2.zip' Content type 'application/zip' length 544615 bytes (531 Kb) opened URL downloaded 531 Kb package 'RSQLite' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\drnevich\Local Settings\Temp\Rtmppth2jw\downloaded_packages updating HTML package descriptions > source("http://bioconductor.org/biocLite.R") > biocLite("Biobase") Running biocinstall version 2.1.7 with R version 2.6.0 (under development) Your version of R requires version 2.1 of Bioconductor. trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/Bio base_1.15.30.zip' Content type 'application/zip' length 2635716 bytes (2.5 Mb) opened URL downloaded 2.5 Mb package 'Biobase' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\drnevich\Local Settings\Temp\Rtmppth2jw\downloaded_packages updating HTML package descriptions > library(Biobase) Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > repos <- biocReposList() > update.packages(repos=repos,ask=FALSE) trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/Ann otationDbi_0.1.12.zip' Content type 'application/zip' length 608740 bytes (594 Kb) opened URL downloaded 594 Kb trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/Cat egory_2.3.30.zip' Content type 'application/zip' length 622607 bytes (608 Kb) opened URL downloaded 608 Kb trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/gen eplotter_1.15.9.zip' Content type 'application/zip' length 1760946 bytes (1.7 Mb) opened URL downloaded 1.7 Mb trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/GOs tats_2.3.16.zip' Content type 'application/zip' length 1683604 bytes (1.6 Mb) opened URL downloaded 1.6 Mb trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/lim ma_2.11.11.zip' Content type 'application/zip' length 1487293 bytes (1.4 Mb) opened URL downloaded 1.4 Mb trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/sim pleaffy_2.13.01.zip' Content type 'application/zip' length 833437 bytes (813 Kb) opened URL downloaded 813 Kb trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/vsn _3.0.14.zip' Content type 'application/zip' length 1978325 bytes (1.9 Mb) opened URL downloaded 1.9 Mb package 'AnnotationDbi' successfully unpacked and MD5 sums checked package 'Category' successfully unpacked and MD5 sums checked package 'geneplotter' successfully unpacked and MD5 sums checked package 'GOstats' successfully unpacked and MD5 sums checked package 'limma' successfully unpacked and MD5 sums checked package 'simpleaffy' successfully unpacked and MD5 sums checked package 'vsn' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\drnevich\Local Settings\Temp\Rtmppth2jw\downloaded_packages updating HTML package descriptions > library(GOstats) Loading required package: graph Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: RSQLite Loading required package: annotate Loading required package: RBGL Loading required package: Category Loading required package: genefilter Loading required package: survival Loading required package: splines > shell.exec("C:/PROGRA~1/R/R-26~1.0DE/library/GOstats/doc/GOstatsHyp erG.pdf") > library("ALL") > library("hgu95av2.db") Attaching package: 'hgu95av2.db' The following object(s) are masked from package:GO.db : db_conn, db_file > library("GO.db") > library("annotate") > library("genefilter") > library("GOstats") > library("RColorBrewer") > library("xtable") > library("Rgraphviz") Attaching package: 'Rgraphviz' The following object(s) are masked from package:annotate : toFile > data(ALL, package = "ALL") > Bcell <- grep("^B", as.character(ALL$BT)) ############################ > bcrAblOrNegIdx <- which(as.character(ALL$mol) %in% c("NEG", subsetType)) Error in inherits(x, "factor") : object "subsetType" not found > subsetType <- "ALL/AF4" ### I added this line of code ############################# > bcrAblOrNegIdx <- which(as.character(ALL$mol) %in% c("NEG", subsetType)) > bcrAblOrNeg <- ALL[, intersect(Bcell, bcrAblOrNegIdx)] > bcrAblOrNeg$mol.biol = factor(bcrAblOrNeg$mol.biol) > entrezIds <- mget(featureNames(bcrAblOrNeg), envir = hgu95av2ENTREZID) > haveEntrezId <- names(entrezIds)[sapply(entrezIds, function(x) !is.na(x))] > numNoEntrezId <- length(featureNames(bcrAblOrNeg)) - length(haveEntrezId) > bcrAblOrNeg <- bcrAblOrNeg[haveEntrezId, ] > haveGo <- sapply(mget(featureNames(bcrAblOrNeg), hgu95av2GO), + function(x) { + if (length(x) == 1 && is.na(x)) + FALSE + else TRUE + }) > numNoGO <- sum(!haveGo) > bcrAblOrNeg <- bcrAblOrNeg[haveGo, ] > iqrCutoff <- 0.5 > bcrAblOrNegIqr <- apply(exprs(bcrAblOrNeg), 1, IQR) > selected <- bcrAblOrNegIqr > iqrCutoff > chrN <- mget(featureNames(bcrAblOrNeg), envir = hgu95av2CHR) > onY <- sapply(chrN, function(x) any(x == "Y")) > onY[is.na(onY)] <- FALSE > selected <- selected & !onY > nsFiltered <- bcrAblOrNeg[selected, ] > numNsWithDups <- length(featureNames(nsFiltered)) > nsFilteredIqr <- bcrAblOrNegIqr[selected] > uniqGenes <- findLargest(featureNames(nsFiltered), nsFilteredIqr, + "hgu95av2") > nsFiltered <- nsFiltered[uniqGenes, ] > numSelected <- length(featureNames(nsFiltered)) > BCRcols = ifelse(nsFiltered$mol == subsetType, "goldenrod", "skyblue") > cols = brewer.pal(10, "RdBu") > affyUniverse <- featureNames(nsFiltered) > entrezUniverse <- unlist(mget(affyUniverse, hgu95av2ENTREZID)) > chipAffyUniverse <- featureNames(bcrAblOrNeg) > chipEntrezUniverse <- mget(chipAffyUniverse, hgu95av2ENTREZID) > chipEntrezUniverse <- unique(unlist(chipEntrezUniverse)) > 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, + universeGeneIds = entrezUniverse, annotation = "hgu95av2.db", + ontology = "BP", pvalueCutoff = hgCutoff, conditional = FALSE, + testDirection = "over") > hgOver <- hyperGTest(params) > hgOver Gene to GO BP test for over-representation 3029 GO BP ids tested (0 have p < 0.001) Selected gene set size: 2889 Gene universe size: 2889 Annotation package: hgu95av2.db > sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-28 r42679) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] Rgraphviz_1.15.5 xtable_1.5-1 RColorBrewer_1.0-1 [4] hgu95av2.db_1.17.3 ALL_1.4.3 GOstats_2.3.16 [7] Category_2.3.30 genefilter_1.15.11 survival_2.32 [10] RBGL_1.13.6 annotate_1.15.6 GO.db_1.17.1 [13] AnnotationDbi_0.1.12 RSQLite_0.6-2 DBI_0.2-3 [16] graph_1.15.14 Biobase_1.15.30 loaded via a namespace (and not attached): [1] cluster_1.11.7 > At 10:52 PM 9/4/2007, Seth Falcon wrote: >Mark W Kimpel <mkimpel at="" iupui.edu=""> writes: > > > Seth and Jenny, > > > > I had the exact same problem last night using code of mine that had > > been working the past year. I updated all packages and the problem > > persisted. I would have reported it but was too busy with something > > that was due today. I am also using R-devel. > >Without more detail it is hard to help further. Note that in >yesterday's build report GOstats passed all its checks which means >that the vignette built. > >Jenny, if you get a chance to update your packages, can you let us >know if that resolves the issue for you? > >+ seth > >-- >Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center >BioC: http://bioconductor.org/ >Blog: http://userprimary.net/user/ Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

>I believe that subseType is in the vignette, but not displayed. Look >at the Rnw file to be sure. This would seem to be a problem for those of us like me who copy and paste from the pdf of the vignette... I forget how you can run a vignette in R *automagically - would you remind me? Yes, I'm being lazy and not wanting to search for it, so a quick pointer somewhere would be fine :) Big thanks, Jenny * one of my favorite words that I learned from using R & BioC!! >Thanks for the update and glad to hear that it is working for you. > >+ seth > >-- >Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center >BioC: http://bioconductor.org/ >Blog: http://userprimary.net/user/