Search
Question: lumi, lumiHumanV2 and GOstats
0
gravatar for Al Ivens
10.5 years ago by
Al Ivens270
Al Ivens270 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" > > > 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_NAM E= C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICA TI 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 -- 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.
ADD COMMENTlink modified 10.5 years ago by James W. MacDonald48k • written 10.5 years ago by Al Ivens270
0
gravatar for James W. MacDonald
10.5 years ago by
United States
James W. MacDonald48k wrote:
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_N AME= > C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFI CATI > 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
ADD COMMENTlink written 10.5 years ago by James W. MacDonald48k
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.
ADD REPLYlink written 10.5 years ago by Al Ivens270
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 351 users visited in the last hour