Question: GO problems with annaffy
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gravatar for Paolo Sirabella
15.7 years ago by
Paolo Sirabella10 wrote:
There appears to be a problem (missing object GOBPID2TERM) with the Gene Ontology metadata (1.5.0) in hgu133a and annaffy (R_1.8.1, Bioconductor_last_release). Hints or suggestions are welcomed. Thank you Follows the history of the problem ... ______________________________________________________________________ _____ > library(annaffy) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Synching your local package management information ... Note: reposTools can not access /usr/lib/R/library. This will not affect your R session unless you wish to install/update/remove packages from this directory Loading required package: GO # Just installed ver. 1.5.0 Loading required package: KEGG > library(hgu133a) > GO() Quality control information for GO Date built: Tue Jan 13 13:48:19 2004 Mappings found for non-probe based rda files: GOBPCHILDREN found 3751 GOBPPARENTS found 8026 GOCCCHILDREN found 452 GOCCPARENTS found 1363 GOGO2LL found 5785 GOLL2GO found 36295 GOMFCHILDREN found 1376 GOMFPARENTS found 7268 GOTERM found 16660 > hgu133a() Quality control information for hgu133a Date built: Wed Jan 14 18:08:05 2004 Number of probes: 22283 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: hgu133aACCNUM found 22283 of 22283 hgu133aCHRLOC found 19717 of 22283 hgu133aCHR found 21080 of 22283 hgu133aENZYME found 2234 of 22283 hgu133aGENENAME found 21130 of 22283 hgu133aGO found 14590 of 22283 hgu133aGRIF found 9806 of 22283 hgu133aHGID found 19257 of 22283 hgu133aLOCUSID found 21481 of 22283 hgu133aMAP found 20993 of 22283 hgu133aNM found 19600 of 22283 hgu133aNP found 19600 of 22283 hgu133aOMIM found 14283 of 22283 hgu133aPATH found 3114 of 22283 hgu133aPMID found 20409 of 22283 hgu133aSUMFUNC found 1293 of 22283 hgu133aSYMBOL found 21130 of 22283 hgu133aUNIGENE found 20620 of 22283 Mappings found for non-probe based rda files: hgu133aENZYME2PROBE found 615 hgu133aGO2ALLPROBES found 4680 hgu133aGO2PROBE found 3459 hgu133aPATH2PROBE found 122 hgu133aPMID2PROBE found 52622 > probeids<-ls(hgu133aSYMBOL) > length(probeids) [1] 22283 > probeids.gos<-aafGO(probeids[1:50],"hgu133a") Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found ______________________________________________________________________ ----------------------------- Paolo Sirabella, PhD University of Rome "La Sapienza" Dept. of Human Physiology and Pharmacology Building of Human Physiology P.le Aldo Moro, 5 - 00185 - Roma - Italy Tel. ++39 06 49910879 Fax ++39 06 233203640 Email paolo.sirabella@uniroma1.it ; psirab@inwind.it Web http://w3.uniroma1.it/cisb/Cisb/members/sirabella Res Non Verba
ADD COMMENTlink modified 15.7 years ago by Jose Duarte100 • written 15.7 years ago by Paolo Sirabella10
Answer: GO problems with annaffy
0
gravatar for Jose Duarte
15.7 years ago by
Jose Duarte100
Jose Duarte100 wrote:
Paolo We had this problem before with the version 1.5 of the metadata packages. See the previous thread in this list: https://www.stat.math.ethz.ch/pipermail/bioconductor/2004-March/004139 .html The solution for me was upgrading to the devel version of annaffy and annotate. Cheers Jose On Thu, 2004-04-08 at 23:40, Paolo Sirabella wrote: > There appears to be a problem (missing object GOBPID2TERM) with the Gene > Ontology metadata (1.5.0) in hgu133a and annaffy (R_1.8.1, > Bioconductor_last_release). > Hints or suggestions are welcomed. > > Thank you > > Follows the history of the problem ... > ____________________________________________________________________ _______ > > > library(annaffy) > Loading required package: Biobase > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > > Synching your local package management information ... > > Note: reposTools can not access /usr/lib/R/library. > This will not affect your R session unless you wish > to install/update/remove packages from this directory > > Loading required package: GO # Just installed ver. 1.5.0 > Loading required package: KEGG > > library(hgu133a) > > GO() > > > Quality control information for GO > Date built: Tue Jan 13 13:48:19 2004 > Mappings found for non-probe based rda files: > GOBPCHILDREN found 3751 > GOBPPARENTS found 8026 > GOCCCHILDREN found 452 > GOCCPARENTS found 1363 > GOGO2LL found 5785 > GOLL2GO found 36295 > GOMFCHILDREN found 1376 > GOMFPARENTS found 7268 > GOTERM found 16660 > > > > > hgu133a() > > > Quality control information for hgu133a > Date built: Wed Jan 14 18:08:05 2004 > Number of probes: 22283 > Probe number missmatch: None > Probe missmatch: None > Mappings found for probe based rda files: > hgu133aACCNUM found 22283 of 22283 > hgu133aCHRLOC found 19717 of 22283 > hgu133aCHR found 21080 of 22283 > hgu133aENZYME found 2234 of 22283 > hgu133aGENENAME found 21130 of 22283 > hgu133aGO found 14590 of 22283 > hgu133aGRIF found 9806 of 22283 > hgu133aHGID found 19257 of 22283 > hgu133aLOCUSID found 21481 of 22283 > hgu133aMAP found 20993 of 22283 > hgu133aNM found 19600 of 22283 > hgu133aNP found 19600 of 22283 > hgu133aOMIM found 14283 of 22283 > hgu133aPATH found 3114 of 22283 > hgu133aPMID found 20409 of 22283 > hgu133aSUMFUNC found 1293 of 22283 > hgu133aSYMBOL found 21130 of 22283 > hgu133aUNIGENE found 20620 of 22283 > Mappings found for non-probe based rda files: > hgu133aENZYME2PROBE found 615 > hgu133aGO2ALLPROBES found 4680 > hgu133aGO2PROBE found 3459 > hgu133aPATH2PROBE found 122 > hgu133aPMID2PROBE found 52622 > > > probeids<-ls(hgu133aSYMBOL) > > length(probeids) > [1] 22283 > > probeids.gos<-aafGO(probeids[1:50],"hgu133a") > Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found > > ______________________________________________________________________ > > ----------------------------- > Paolo Sirabella, PhD > University of Rome "La Sapienza" > Dept. of Human Physiology and Pharmacology > Building of Human Physiology > P.le Aldo Moro, 5 - 00185 - Roma - Italy > Tel. ++39 06 49910879 > Fax ++39 06 233203640 > Email paolo.sirabella@uniroma1.it ; psirab@inwind.it > Web http://w3.uniroma1.it/cisb/Cisb/members/sirabella > > Res Non Verba > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Jose Duarte <jose.duarte@anat.ox.ac.uk>
ADD COMMENTlink written 15.7 years ago by Jose Duarte100
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