Hi Jim, Ah. That explains it, many thanks. And no, biocLite wasnt guilty! Cheers, a > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: 29 May 2008 14:44 > To: Al Ivens > Cc: 'bioc' > Subject: Re: [BioC] lumi, lumiHumanV2 and GOstats > > > Hi Al, > > Al Ivens wrote: > > Hi all, > > > > I have been trying out the GOstats section of the lumi > vignette, using > > data obtained from Illumina WG6 chips. I use the > lumiHumanV2 package. > > > > I have two installations of R and Bioconductor: > > > > 1. On my Windoze laptop, I have R 2.6.2 and as far as I am > aware, up > > to date versions of the relevant Bioconductor packages for 2.6.2. > > Doing the GOstats works just fine. 2. On my Unix server, I have R > > 2.7.0, and as far as I am aware, the most up to date Bioc > packages. > > Doing the GOstats on this platform, using the same GOstats > script etc, > > doesn't work. > > > > Below is the error, traceback and sessionInfo. At a bit of > loss as to > > why the difference! > > > > Cheers and thanks in advance for any assistance, > > > > a > > > > X--------------------------------------------------------- > > Error in do.call(paste(pname, "dbconn", sep = "_"), list()) : > > could not find function "lumiHumanV2_dbconn" > > This is because there isn't a lumiHumanV2 in BioC 2.2. Not > sure how you > got this installed, as biocLite() shouldn't have done so. > > Anyway, I believe you want the lumiHumanAll.db package (and to remove > the lumiHumanV2 package, as that is from an older BioC release). > > Best, > > Jim > > > >> > >> traceback() > > 8: do.call(paste(pname, "dbconn", sep = "_"), list()) > > 7: getGoToEntrezMap_db(p) > > 6: categoryToEntrezBuilder(p) > > 5: categoryToEntrezBuilder(p) > > 4: is(object, Cl) > > 3: is(object, Cl) > > 2: .valueClassTest(standardGeneric("hyperGTest"), > "HyperGResultBase", > > "hyperGTest") > > 1: hyperGTest(BPparams) > >> sessionInfo() > > R version 2.7.0 (2008-04-22) > > x86_64-pc-linux-gnu > > > > locale: > > > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB > > .U > > > TF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF- > 8;LC_NAME= > > > C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_ID > ENTIFICATI > > ON=C > > > > attached base packages: > > [1] grid splines tools stats graphics > grDevices utils > > > > [8] datasets methods base > > > > other attached packages: > > [1] arrayQualityMetrics_1.6.0 beadarray_1.8.0 > > [3] latticeExtra_0.3-1 simpleaffy_2.16.0 > > [5] affyPLM_1.16.0 gcrma_2.12.0 > > [7] matchprobes_1.12.0 RColorBrewer_1.0-2 > > [9] vsn_3.6.0 geneplotter_1.18.0 > > [11] lattice_0.17-2 gplots_2.6.0 > > [13] gdata_2.4.1 gtools_2.4.0 > > [15] limma_2.14.1 GOstats_2.6.0 > > [17] Category_2.6.0 genefilter_1.20.0 > > [19] survival_2.34 RBGL_1.16.0 > > [21] annotate_1.18.0 xtable_1.5-2 > > [23] GO.db_2.2.0 AnnotationDbi_1.2.1 > > [25] RSQLite_0.6-8 DBI_0.2-4 > > [27] graph_1.18.1 lumiHumanV2_1.3.1 > > [29] lumi_1.6.0 mgcv_1.3-31 > > [31] affy_1.18.0 preprocessCore_1.2.0 > > [33] affyio_1.8.0 Biobase_2.0.1 > > > > loaded via a namespace (and not attached): > > [1] cluster_1.11.9 KernSmooth_2.22-21 > > > > > > > > > > -- > 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 > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.