exonmap/xmapcore error
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anupam sinha ▴ 270
@anupam-sinha-3207
Last seen 8.2 years ago
Dear all, I have been learning to use exonmap/xmapcore from the tutorial ""Comprehensive analysis of Affymetrix Exon arrays Using BioConductor" . But I have run into some problems. I have installed "xmapcore_homo_sapiens_58" on my system as per instructions . Do I also have to install ensemble and old exonmap databases? Can someone help me out ? Thanks in advance for any suggestions. > library(xmapcore) > library(exonmap) Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Attaching package: 'Biobase' The following object(s) are masked from 'package:IRanges': updateObject Loading required package: genefilter Loading required package: RColorBrewer Attaching package: 'exonmap' The following object(s) are masked from 'package:xmapcore': exon.details, exon.to.gene, exon.to.probeset, exon.to.transcript, exonic, exons.in.range, gene.details, gene.to.exon, gene.to.probeset, gene.to.transcript, genes.in.range, intergenic, intronic, is.exonic, is.intergenic, is.intronic, probes.in.range, probeset.to.exon, probeset.to.gene, probeset.to.probe, probeset.to.transcript, probesets.in.range, symbol.to.gene, transcript.details, transcript.to.exon, transcript.to.gene, transcript.to.probeset, transcripts.in.range > setwd("/home/aragorn/R_Workspace/ExonarraysMCF7andMCF10Adata_cel/") > raw.data<-read.exon() > raw.data@cdfName<-"exon.pmcdf" > x.rma<-rma(raw.data) Background correcting Normalizing Calculating Expression > pc.rma<-pc(x.rma,"group",c("a","b")) > keep<-(abs(fc(pc.rma))>1)&tt(pc.rma)< 1e-4 > sigs<-featureNames(x.rma)[keep] > xmapConnect() Select a database to connect to: 1: Hman ('xmapcore_homo_sapiens_58') Selection: 1 password: Warning message: In .xmap.load.config() : Environment 'R_XMAP_CONF_DIR' not set. Please refer to INSTALL.TXT for information on how to set this up. Trying '.exonmap'. > probeset.to.exon(sigs[1:5]) *Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: PROCEDURE xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* > xmapConnect() Select a database to connect to: 1: Hman ('xmapcore_homo_sapiens_58') Selection: 1 > probeset.to.exon(sigs[1:5]) Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: PROCEDURE xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist) > xmap.connect() password: Disconnecting from xmapcore_homo_sapiens_58 (localhost) Connected to xmapcore_homo_sapiens_58 (localhost) Selected array 'HuEx-1_0' as a default. > probeset.to.exon(sigs[1:5]) *Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: PROCEDURE xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-redhat-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] exon.pmcdf_1.1 exonmap_2.6.0 RColorBrewer_1.0-2 genefilter_1.30.0 [5] affy_1.26.1 Biobase_2.8.0 xmapcore_1.2.5 digest_0.4.2 [9] IRanges_1.6.8 RMySQL_0.7-4 DBI_0.2-5 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 [4] preprocessCore_1.10.0 RSQLite_0.9-1 splines_2.11.0 [7] survival_2.35-8 tcltk_2.11.0 tools_2.11.0 [10] xtable_1.5-6 Regards, Anupam -- Graduate Student, Center For DNA Fingerprinting And Diagnostics, 4-1-714 to 725/2, Tuljaguda complex Mozamzahi Road, Nampally, Hyderabad-500001 [[alternative HTML version deleted]]
exonmap exonmap • 1.3k views
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@james-w-macdonald-5106
Last seen 7 hours ago
United States
Hi Anupam, On 7/20/2010 12:00 PM, anupam sinha wrote: > Dear all, > I have been learning to use exonmap/xmapcore from the > tutorial ""Comprehensive analysis of Affymetrix Exon arrays Using > BioConductor" . > But I have run into some problems. I have installed > "xmapcore_homo_sapiens_58" on my system as per instructions . > Do I also have to install ensemble and old exonmap databases? Can > someone help me out ? Thanks in advance for any suggestions. > > >> library(xmapcore) >> library(exonmap) > Loading required package: affy > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > Attaching package: 'Biobase' > > The following object(s) are masked from 'package:IRanges': > > updateObject > > Loading required package: genefilter > Loading required package: RColorBrewer > > Attaching package: 'exonmap' > > The following object(s) are masked from 'package:xmapcore': > > exon.details, exon.to.gene, exon.to.probeset, exon.to.transcript, > exonic, exons.in.range, gene.details, gene.to.exon, > gene.to.probeset, gene.to.transcript, genes.in.range, intergenic, > intronic, is.exonic, is.intergenic, is.intronic, probes.in.range, > probeset.to.exon, probeset.to.gene, probeset.to.probe, > probeset.to.transcript, probesets.in.range, symbol.to.gene, > transcript.details, transcript.to.exon, transcript.to.gene, > transcript.to.probeset, transcripts.in.range > > >> setwd("/home/aragorn/R_Workspace/ExonarraysMCF7andMCF10Adata_cel/") >> raw.data<-read.exon() >> raw.data at cdfName<-"exon.pmcdf" >> x.rma<-rma(raw.data) > Background correcting > Normalizing > Calculating Expression >> pc.rma<-pc(x.rma,"group",c("a","b")) >> keep<-(abs(fc(pc.rma))>1)&tt(pc.rma)< 1e-4 >> sigs<-featureNames(x.rma)[keep] >> xmapConnect() > Select a database to connect to: > > 1: Hman ('xmapcore_homo_sapiens_58') > > Selection: 1 > password: > Warning message: > In .xmap.load.config() : > Environment 'R_XMAP_CONF_DIR' not set. Please refer to INSTALL.TXT for > information on how to set this up. You have to correct this error first. You say you installed '"xmapcore_homo_sapiens_58" on my system as per instructions', but I don't know what that means. There is an INSTALL.txt that comes with the xmapcore database dump that you need to follow, and an INSTALL.pdf that comes with exonmap that you need to follow as well. Obviously you missed at least one step, so I would recommend re- visiting these documents and ensuring that you followed them exactly. Best, Jim > > Trying '.exonmap'. > >> probeset.to.exon(sigs[1:5]) > *Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* >> xmapConnect() > Select a database to connect to: > > 1: Hman ('xmapcore_homo_sapiens_58') > > Selection: 1 > >> probeset.to.exon(sigs[1:5]) > Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist) > >> xmap.connect() > password: > Disconnecting from xmapcore_homo_sapiens_58 (localhost) > Connected to xmapcore_homo_sapiens_58 (localhost) > Selected array 'HuEx-1_0' as a default. >> probeset.to.exon(sigs[1:5]) > *Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* >> sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-redhat-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] exon.pmcdf_1.1 exonmap_2.6.0 RColorBrewer_1.0-2 > genefilter_1.30.0 > [5] affy_1.26.1 Biobase_2.8.0 xmapcore_1.2.5 > digest_0.4.2 > [9] IRanges_1.6.8 RMySQL_0.7-4 DBI_0.2-5 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 > [4] preprocessCore_1.10.0 RSQLite_0.9-1 splines_2.11.0 > [7] survival_2.35-8 tcltk_2.11.0 tools_2.11.0 > [10] xtable_1.5-6 > > Regards, > > Anupam -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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Paul Leo ▴ 970
@paul-leo-2092
Last seen 8.2 years ago
Yeah originally, they did a pretty poor job at describing how to do that, it was the largest impediment to otherwise using a very nice package. They threw you to the wolves by pointing to a section that describes how to entire the whole ensemble DB and web interface. I notice they have the new xmapcore database , are those the ones you are using?: http://xmap.picr.man.ac.uk/download/index#hsxmapcore I have NOT used those but at least in the beginning of the year , You only need SQL to install ,you do not need to install ensemble , just the "core" data base. As I recall you need to go into the SQl and get create the database then you need to run the script that makes the tables. Then these are filled (but a second script, cat's recall) my notes indicate I also inatall exon.pmcdf: (in above web link) R CMD INSTALL --clean exon.pmcdf_1.1.tar.gz you may need to run something like this on the command line first to start the service: mysql -h host_computer -u xmap -pPassword ## where the host_compueter is where the db is and Password is the password) then in R xmapConnect("human") ################## In my home directory there is a .exnmap file with: a file database.txt attached and a subfolder db.local that has a file starts.core.homo_sapiens_core_56_37a.R a larget 3.7Mb file and in bashrc: export XMAP_BRIDGE_CACHE=/home/pleo/.xmb_cache ####### I think now with the new core database you might be better off using documentation in the latest exonmap or xmapcore libraries than that original manuscript. They have made some changes. Hope that helps Paul -----Original Message----- From: anupam sinha <anupam.contact@gmail.com> To: bioc <bioconductor at="" stat.math.ethz.ch=""> Subject: [BioC] exonmap/xmapcore error Date: Tue, 20 Jul 2010 21:30:24 +0530 Dear all, I have been learning to use exonmap/xmapcore from the tutorial ""Comprehensive analysis of Affymetrix Exon arrays Using BioConductor" . But I have run into some problems. I have installed "xmapcore_homo_sapiens_58" on my system as per instructions . Do I also have to install ensemble and old exonmap databases? Can someone help me out ? Thanks in advance for any suggestions. > library(xmapcore) > library(exonmap) Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Attaching package: 'Biobase' The following object(s) are masked from 'package:IRanges': updateObject Loading required package: genefilter Loading required package: RColorBrewer Attaching package: 'exonmap' The following object(s) are masked from 'package:xmapcore': exon.details, exon.to.gene, exon.to.probeset, exon.to.transcript, exonic, exons.in.range, gene.details, gene.to.exon, gene.to.probeset, gene.to.transcript, genes.in.range, intergenic, intronic, is.exonic, is.intergenic, is.intronic, probes.in.range, probeset.to.exon, probeset.to.gene, probeset.to.probe, probeset.to.transcript, probesets.in.range, symbol.to.gene, transcript.details, transcript.to.exon, transcript.to.gene, transcript.to.probeset, transcripts.in.range > setwd("/home/aragorn/R_Workspace/ExonarraysMCF7andMCF10Adata_cel/") > raw.data<-read.exon() > raw.data at cdfName<-"exon.pmcdf" > x.rma<-rma(raw.data) Background correcting Normalizing Calculating Expression > pc.rma<-pc(x.rma,"group",c("a","b")) > keep<-(abs(fc(pc.rma))>1)&tt(pc.rma)< 1e-4 > sigs<-featureNames(x.rma)[keep] > xmapConnect() Select a database to connect to: 1: Hman ('xmapcore_homo_sapiens_58') Selection: 1 password: Warning message: In .xmap.load.config() : Environment 'R_XMAP_CONF_DIR' not set. Please refer to INSTALL.TXT for information on how to set this up. Trying '.exonmap'. > probeset.to.exon(sigs[1:5]) *Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: PROCEDURE xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* > xmapConnect() Select a database to connect to: 1: Hman ('xmapcore_homo_sapiens_58') Selection: 1 > probeset.to.exon(sigs[1:5]) Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: PROCEDURE xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist) > xmap.connect() password: Disconnecting from xmapcore_homo_sapiens_58 (localhost) Connected to xmapcore_homo_sapiens_58 (localhost) Selected array 'HuEx-1_0' as a default. > probeset.to.exon(sigs[1:5]) *Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: PROCEDURE xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-redhat-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] exon.pmcdf_1.1 exonmap_2.6.0 RColorBrewer_1.0-2 genefilter_1.30.0 [5] affy_1.26.1 Biobase_2.8.0 xmapcore_1.2.5 digest_0.4.2 [9] IRanges_1.6.8 RMySQL_0.7-4 DBI_0.2-5 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 [4] preprocessCore_1.10.0 RSQLite_0.9-1 splines_2.11.0 [7] survival_2.35-8 tcltk_2.11.0 tools_2.11.0 [10] xtable_1.5-6 Regards, Anupam -- Graduate Student, Center For DNA Fingerprinting And Diagnostics, 4-1-714 to 725/2, Tuljaguda complex Mozamzahi Road, Nampally, Hyderabad-500001 [[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 -------------- next part -------------- "name" "species" "db.name" "type" "host" "port" "username" "password" "human" "homo_sapiens" "homo_sapiens_core_56_37a" "core" "bioinform02-ubuntu" "" "xmap" "VbIR3y"
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Hi Paul, Hopefully it's simpler now - with xmapcore, you need to install just the xmapcore database into a working MySQL instance (and the package itself, of course). There's also a pretty detailed walk through in the INSTALL.pdf document that forms part of the xmapcore package. Crispin > > Yeah originally, they did a pretty poor job at describing how to do > that, it was the largest impediment to otherwise using a very nice > package. They threw you to the wolves by pointing to a section that > describes how to entire the whole ensemble DB and web interface. I > notice they have the new xmapcore database , are those the ones you are > using?: > > http://xmap.picr.man.ac.uk/download/index#hsxmapcore > > I have NOT used those > > but at least in the beginning of the year , You only need SQL to > install ,you do not need to install ensemble , just the "core" data > base. > As I recall you need to go into the SQl and get create the database > then you need to run the script that makes the tables. > Then these are filled (but a second script, cat's recall) > > my notes indicate I also inatall exon.pmcdf: (in above web link) > R CMD INSTALL --clean exon.pmcdf_1.1.tar.gz > > > > you may need to run something like this on the command line first to > start the service: > > mysql -h host_computer -u xmap -pPassword ## where the host_compueter is > where the db is and Password is the password) > > then in R > > xmapConnect("human") > > > ################## > In my home directory there is a .exnmap file with: > a file database.txt attached > > and a subfolder db.local that has > a file starts.core.homo_sapiens_core_56_37a.R a larget 3.7Mb file > > and in bashrc: > export XMAP_BRIDGE_CACHE=/home/pleo/.xmb_cache > ####### > > I think now with the new core database you might be better off using > documentation in the latest exonmap or xmapcore libraries than that original > manuscript. They have made some changes. > > Hope that helps > Paul > > > > -----Original Message----- > From: anupam sinha <anupam.contact@gmail.com> > To: bioc <bioconductor@stat.math.ethz.ch> > Subject: [BioC] exonmap/xmapcore error > Date: Tue, 20 Jul 2010 21:30:24 +0530 > > > Dear all, > I have been learning to use exonmap/xmapcore from the > tutorial ""Comprehensive analysis of Affymetrix Exon arrays Using > BioConductor" . > But I have run into some problems. I have installed > "xmapcore_homo_sapiens_58" on my system as per instructions . > Do I also have to install ensemble and old exonmap databases? Can > someone help me out ? Thanks in advance for any suggestions. > > >> > library(xmapcore) >> > library(exonmap) > Loading required package: affy > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > Attaching package: 'Biobase' > > The following object(s) are masked from 'package:IRanges': > > updateObject > > Loading required package: genefilter > Loading required package: RColorBrewer > > Attaching package: 'exonmap' > > The following object(s) are masked from 'package:xmapcore': > > exon.details, exon.to.gene, exon.to.probeset, exon.to.transcript, > exonic, exons.in.range, gene.details, gene.to.exon, > gene.to.probeset, gene.to.transcript, genes.in.range, intergenic, > intronic, is.exonic, is.intergenic, is.intronic, probes.in.range, > probeset.to.exon, probeset.to.gene, probeset.to.probe, > probeset.to.transcript, probesets.in.range, symbol.to.gene, > transcript.details, transcript.to.exon, transcript.to.gene, > transcript.to.probeset, transcripts.in.range > > >> > setwd("/home/aragorn/R_Workspace/ExonarraysMCF7andMCF10Adata_cel/") >> > raw.data<-read.exon() >> > raw.data@cdfName<-"exon.pmcdf" >> > x.rma<-rma(raw.data) > Background correcting > Normalizing > Calculating Expression >> > pc.rma<-pc(x.rma,"group",c("a","b")) >> > keep<-(abs(fc(pc.rma))>1)&tt(pc.rma)< 1e-4 >> > sigs<-featureNames(x.rma)[keep] >> > xmapConnect() > Select a database to connect to: > > 1: Hman ('xmapcore_homo_sapiens_58') > > Selection: 1 > password: > Warning message: > In .xmap.load.config() : > Environment 'R_XMAP_CONF_DIR' not set. Please refer to INSTALL.TXT for > information on how to set this up. > > Trying '.exonmap'. > >> > probeset.to.exon(sigs[1:5]) > *Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* >> > xmapConnect() > Select a database to connect to: > > 1: Hman ('xmapcore_homo_sapiens_58') > > Selection: 1 > >> > probeset.to.exon(sigs[1:5]) > Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist) > >> > xmap.connect() > password: > Disconnecting from xmapcore_homo_sapiens_58 (localhost) > Connected to xmapcore_homo_sapiens_58 (localhost) > Selected array 'HuEx-1_0' as a default. >> > probeset.to.exon(sigs[1:5]) > *Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* >> > sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-redhat-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] exon.pmcdf_1.1 exonmap_2.6.0 RColorBrewer_1.0-2 > genefilter_1.30.0 > [5] affy_1.26.1 Biobase_2.8.0 xmapcore_1.2.5 > digest_0.4.2 > [9] IRanges_1.6.8 RMySQL_0.7-4 DBI_0.2-5 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 > [4] preprocessCore_1.10.0 RSQLite_0.9-1 splines_2.11.0 > [7] survival_2.35-8 tcltk_2.11.0 tools_2.11.0 > [10] xtable_1.5-6 > > Regards, > > Anupam > -- > Graduate Student, > Center For DNA Fingerprinting And Diagnostics, > 4-1-714 to 725/2, Tuljaguda complex > Mozamzahi Road, Nampally, > Hyderabad-500001 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:15}}
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Hi Crispin, Great that those changes have been made. Exonmap proved to be very elegant package and useful package for us. I should say that initial problems we had on installing the old version, though frustrating, the were worth the effort. I look forward to trying out the new kit! Cheers Paul -----Original Message----- From: Crispin Miller <cmiller@picr.man.ac.uk> To: Bioconductor <bioconductor@stat.math.ethz.ch> Subject: Re: [BioC] exonmap/xmapcore error Date: Thu, 22 Jul 2010 14:09:55 +0100 Hi Paul, Hopefully it's simpler now - with xmapcore, you need to install just the xmapcore database into a working MySQL instance (and the package itself, of course). There's also a pretty detailed walk through in the INSTALL.pdf document that forms part of the xmapcore package. Crispin > > Yeah originally, they did a pretty poor job at describing how to do > that, it was the largest impediment to otherwise using a very nice > package. They threw you to the wolves by pointing to a section that > describes how to entire the whole ensemble DB and web interface. I > notice they have the new xmapcore database , are those the ones you are > using?: > > http://xmap.picr.man.ac.uk/download/index#hsxmapcore > > I have NOT used those > > but at least in the beginning of the year , You only need SQL to > install ,you do not need to install ensemble , just the "core" data > base. > As I recall you need to go into the SQl and get create the database > then you need to run the script that makes the tables. > Then these are filled (but a second script, cat's recall) > > my notes indicate I also inatall exon.pmcdf: (in above web link) > R CMD INSTALL --clean exon.pmcdf_1.1.tar.gz > > > > you may need to run something like this on the command line first to > start the service: > > mysql -h host_computer -u xmap -pPassword ## where the host_compueter is > where the db is and Password is the password) > > then in R > > xmapConnect("human") > > > ################## > In my home directory there is a .exnmap file with: > a file database.txt attached > > and a subfolder db.local that has > a file starts.core.homo_sapiens_core_56_37a.R a larget 3.7Mb file > > and in bashrc: > export XMAP_BRIDGE_CACHE=/home/pleo/.xmb_cache > ####### > > I think now with the new core database you might be better off using > documentation in the latest exonmap or xmapcore libraries than that original > manuscript. They have made some changes. > > Hope that helps > Paul > > > > -----Original Message----- > From: anupam sinha <anupam.contact@gmail.com> > To: bioc <bioconductor@stat.math.ethz.ch> > Subject: [BioC] exonmap/xmapcore error > Date: Tue, 20 Jul 2010 21:30:24 +0530 > > > Dear all, > I have been learning to use exonmap/xmapcore from the > tutorial ""Comprehensive analysis of Affymetrix Exon arrays Using > BioConductor" . > But I have run into some problems. I have installed > "xmapcore_homo_sapiens_58" on my system as per instructions . > Do I also have to install ensemble and old exonmap databases? Can > someone help me out ? Thanks in advance for any suggestions. > > >> > library(xmapcore) >> > library(exonmap) > Loading required package: affy > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > Attaching package: 'Biobase' > > The following object(s) are masked from 'package:IRanges': > > updateObject > > Loading required package: genefilter > Loading required package: RColorBrewer > > Attaching package: 'exonmap' > > The following object(s) are masked from 'package:xmapcore': > > exon.details, exon.to.gene, exon.to.probeset, exon.to.transcript, > exonic, exons.in.range, gene.details, gene.to.exon, > gene.to.probeset, gene.to.transcript, genes.in.range, intergenic, > intronic, is.exonic, is.intergenic, is.intronic, probes.in.range, > probeset.to.exon, probeset.to.gene, probeset.to.probe, > probeset.to.transcript, probesets.in.range, symbol.to.gene, > transcript.details, transcript.to.exon, transcript.to.gene, > transcript.to.probeset, transcripts.in.range > > >> > setwd("/home/aragorn/R_Workspace/ExonarraysMCF7andMCF10Adata_cel/") >> > raw.data<-read.exon() >> > raw.data@cdfName<-"exon.pmcdf" >> > x.rma<-rma(raw.data) > Background correcting > Normalizing > Calculating Expression >> > pc.rma<-pc(x.rma,"group",c("a","b")) >> > keep<-(abs(fc(pc.rma))>1)&tt(pc.rma)< 1e-4 >> > sigs<-featureNames(x.rma)[keep] >> > xmapConnect() > Select a database to connect to: > > 1: Hman ('xmapcore_homo_sapiens_58') > > Selection: 1 > password: > Warning message: > In .xmap.load.config() : > Environment 'R_XMAP_CONF_DIR' not set. Please refer to INSTALL.TXT for > information on how to set this up. > > Trying '.exonmap'. > >> > probeset.to.exon(sigs[1:5]) > *Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* >> > xmapConnect() > Select a database to connect to: > > 1: Hman ('xmapcore_homo_sapiens_58') > > Selection: 1 > >> > probeset.to.exon(sigs[1:5]) > Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist) > >> > xmap.connect() > password: > Disconnecting from xmapcore_homo_sapiens_58 (localhost) > Connected to xmapcore_homo_sapiens_58 (localhost) > Selected array 'HuEx-1_0' as a default. >> > probeset.to.exon(sigs[1:5]) > *Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* >> > sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-redhat-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] exon.pmcdf_1.1 exonmap_2.6.0 RColorBrewer_1.0-2 > genefilter_1.30.0 > [5] affy_1.26.1 Biobase_2.8.0 xmapcore_1.2.5 > digest_0.4.2 > [9] IRanges_1.6.8 RMySQL_0.7-4 DBI_0.2-5 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 > [4] preprocessCore_1.10.0 RSQLite_0.9-1 splines_2.11.0 > [7] survival_2.35-8 tcltk_2.11.0 tools_2.11.0 > [10] xtable_1.5-6 > > Regards, > > Anupam > -- > Graduate Student, > Center For DNA Fingerprinting And Diagnostics, > 4-1-714 to 725/2, Tuljaguda complex > Mozamzahi Road, Nampally, > Hyderabad-500001 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:11}}
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Hi Paul and Crispin, Thanks a lot for your suggetsions. Regards, Anupam On Fri, Jul 23, 2010 at 5:33 AM, Paul Leo <p.leo@uq.edu.au> wrote: > Hi Crispin, > Great that those changes have been made. Exonmap proved to be very > elegant package and useful package for us. > I should say that initial problems we had on installing the old version, > though frustrating, the were worth the effort. I look forward to trying > out the new kit! > > Cheers > Paul > > > > > > -----Original Message----- > From: Crispin Miller <cmiller@picr.man.ac.uk> > To: Bioconductor <bioconductor@stat.math.ethz.ch> > Subject: Re: [BioC] exonmap/xmapcore error > Date: Thu, 22 Jul 2010 14:09:55 +0100 > > > Hi Paul, > > Hopefully it's simpler now - with xmapcore, you need to install just the > xmapcore database into a working MySQL instance (and the package itself, of > course). > > There's also a pretty detailed walk through in the INSTALL.pdf document > that > forms part of the xmapcore package. > > Crispin > > > > > Yeah originally, they did a pretty poor job at describing how to do > > that, it was the largest impediment to otherwise using a very nice > > package. They threw you to the wolves by pointing to a section that > > describes how to entire the whole ensemble DB and web interface. I > > notice they have the new xmapcore database , are those the ones you are > > using?: > > > > http://xmap.picr.man.ac.uk/download/index#hsxmapcore > > > > I have NOT used those > > > > but at least in the beginning of the year , You only need SQL to > > install ,you do not need to install ensemble , just the "core" data > > base. > > As I recall you need to go into the SQl and get create the database > > then you need to run the script that makes the tables. > > Then these are filled (but a second script, cat's recall) > > > > my notes indicate I also inatall exon.pmcdf: (in above web link) > > R CMD INSTALL --clean exon.pmcdf_1.1.tar.gz > > > > > > > > you may need to run something like this on the command line first to > > start the service: > > > > mysql -h host_computer -u xmap -pPassword ## where the host_compueter is > > where the db is and Password is the password) > > > > then in R > > > > xmapConnect("human") > > > > > > ################## > > In my home directory there is a .exnmap file with: > > a file database.txt attached > > > > and a subfolder db.local that has > > a file starts.core.homo_sapiens_core_56_37a.R a larget 3.7Mb file > > > > and in bashrc: > > export XMAP_BRIDGE_CACHE=/home/pleo/.xmb_cache > > ####### > > > > I think now with the new core database you might be better off using > > documentation in the latest exonmap or xmapcore libraries than that > original > > manuscript. They have made some changes. > > > > Hope that helps > > Paul > > > > > > > > -----Original Message----- > > From: anupam sinha <anupam.contact@gmail.com> > > To: bioc <bioconductor@stat.math.ethz.ch> > > Subject: [BioC] exonmap/xmapcore error > > Date: Tue, 20 Jul 2010 21:30:24 +0530 > > > > > > Dear all, > > I have been learning to use exonmap/xmapcore from the > > tutorial ""Comprehensive analysis of Affymetrix Exon arrays Using > > BioConductor" . > > But I have run into some problems. I have installed > > "xmapcore_homo_sapiens_58" on my system as per instructions . > > Do I also have to install ensemble and old exonmap databases? Can > > someone help me out ? Thanks in advance for any suggestions. > > > > > >> > library(xmapcore) > >> > library(exonmap) > > Loading required package: affy > > Loading required package: Biobase > > > > Welcome to Bioconductor > > > > Vignettes contain introductory material. To view, type > > 'openVignette()'. To cite Bioconductor, see > > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > > > > Attaching package: 'Biobase' > > > > The following object(s) are masked from 'package:IRanges': > > > > updateObject > > > > Loading required package: genefilter > > Loading required package: RColorBrewer > > > > Attaching package: 'exonmap' > > > > The following object(s) are masked from 'package:xmapcore': > > > > exon.details, exon.to.gene, exon.to.probeset, exon.to.transcript, > > exonic, exons.in.range, gene.details, gene.to.exon, > > gene.to.probeset, gene.to.transcript, genes.in.range, intergenic, > > intronic, is.exonic, is.intergenic, is.intronic, probes.in.range, > > probeset.to.exon, probeset.to.gene, probeset.to.probe, > > probeset.to.transcript, probesets.in.range, symbol.to.gene, > > transcript.details, transcript.to.exon, transcript.to.gene, > > transcript.to.probeset, transcripts.in.range > > > > > >> > setwd("/home/aragorn/R_Workspace/ExonarraysMCF7andMCF10Adata_cel/") > >> > raw.data<-read.exon() > >> > raw.data@cdfName<-"exon.pmcdf" > >> > x.rma<-rma(raw.data) > > Background correcting > > Normalizing > > Calculating Expression > >> > pc.rma<-pc(x.rma,"group",c("a","b")) > >> > keep<-(abs(fc(pc.rma))>1)&tt(pc.rma)< 1e-4 > >> > sigs<-featureNames(x.rma)[keep] > >> > xmapConnect() > > Select a database to connect to: > > > > 1: Hman ('xmapcore_homo_sapiens_58') > > > > Selection: 1 > > password: > > Warning message: > > In .xmap.load.config() : > > Environment 'R_XMAP_CONF_DIR' not set. Please refer to INSTALL.TXT for > > information on how to set this up. > > > > Trying '.exonmap'. > > > >> > probeset.to.exon(sigs[1:5]) > > *Error in mysqlExecStatement(conn, statement, ...) : > > RS-DBI driver: (could not run statement: PROCEDURE > > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* > >> > xmapConnect() > > Select a database to connect to: > > > > 1: Hman ('xmapcore_homo_sapiens_58') > > > > Selection: 1 > > > >> > probeset.to.exon(sigs[1:5]) > > Error in mysqlExecStatement(conn, statement, ...) : > > RS-DBI driver: (could not run statement: PROCEDURE > > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist) > > > >> > xmap.connect() > > password: > > Disconnecting from xmapcore_homo_sapiens_58 (localhost) > > Connected to xmapcore_homo_sapiens_58 (localhost) > > Selected array 'HuEx-1_0' as a default. > >> > probeset.to.exon(sigs[1:5]) > > *Error in mysqlExecStatement(conn, statement, ...) : > > RS-DBI driver: (could not run statement: PROCEDURE > > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* > >> > sessionInfo() > > R version 2.11.0 (2010-04-22) > > x86_64-redhat-linux-gnu > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] exon.pmcdf_1.1 exonmap_2.6.0 RColorBrewer_1.0-2 > > genefilter_1.30.0 > > [5] affy_1.26.1 Biobase_2.8.0 xmapcore_1.2.5 > > digest_0.4.2 > > [9] IRanges_1.6.8 RMySQL_0.7-4 DBI_0.2-5 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 > > [4] preprocessCore_1.10.0 RSQLite_0.9-1 splines_2.11.0 > > [7] survival_2.35-8 tcltk_2.11.0 tools_2.11.0 > > [10] xtable_1.5-6 > > > > Regards, > > > > Anupam > > -- > > Graduate Student, > > Center For DNA Fingerprinting And Diagnostics, > > 4-1-714 to 725/2, Tuljaguda complex > > Mozamzahi Road, Nampally, > > Hyderabad-500001 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -------------------------------------------------------- > This email is confidential and intended solely for the...{{dropped:23}}
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 8.2 years ago
Dear Anupam, Since we published exonmap, we've released a newer package, xmapcore. This focuses on the core database connectivity and has a significant amount of work done behind the API to make certain bits of it much much quicker. We'll put a note in the exonmap vignette to point people to the new package, since it's obviously causing a bit of confusion. One thing that xmapcore does is use a smaller database that's been optimised for some of the queries that were slower in exonmap than we would have liked - this also means that you no longer have to install Ensembl - the xmapcore database, on it's own, will do the job. Have a look at the documentation for the xmapcore package (especially INSTALL.pdf) that provides step-by-step installation instructions. As we mention in the exonmap vignette, there were some basic utility functions to help people load and begin to explore exon array data. As you'll see from the vignette, we've not duplicated these in xmapcore. Crispin On 20/07/2010 17:00, "anupam sinha" <anupam.contact@gmail.com> wrote: > Dear all, > I have been learning to use exonmap/xmapcore from the > tutorial ""Comprehensive analysis of Affymetrix Exon arrays Using > BioConductor" . > But I have run into some problems. I have installed > "xmapcore_homo_sapiens_58" on my system as per instructions . > Do I also have to install ensemble and old exonmap databases? Can > someone help me out ? Thanks in advance for any suggestions. > > >> > library(xmapcore) >> > library(exonmap) > Loading required package: affy > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > Attaching package: 'Biobase' > > The following object(s) are masked from 'package:IRanges': > > updateObject > > Loading required package: genefilter > Loading required package: RColorBrewer > > Attaching package: 'exonmap' > > The following object(s) are masked from 'package:xmapcore': > > exon.details, exon.to.gene, exon.to.probeset, exon.to.transcript, > exonic, exons.in.range, gene.details, gene.to.exon, > gene.to.probeset, gene.to.transcript, genes.in.range, intergenic, > intronic, is.exonic, is.intergenic, is.intronic, probes.in.range, > probeset.to.exon, probeset.to.gene, probeset.to.probe, > probeset.to.transcript, probesets.in.range, symbol.to.gene, > transcript.details, transcript.to.exon, transcript.to.gene, > transcript.to.probeset, transcripts.in.range > > >> > setwd("/home/aragorn/R_Workspace/ExonarraysMCF7andMCF10Adata_cel/") >> > raw.data<-read.exon() >> > raw.data@cdfName<-"exon.pmcdf" >> > x.rma<-rma(raw.data) > Background correcting > Normalizing > Calculating Expression >> > pc.rma<-pc(x.rma,"group",c("a","b")) >> > keep<-(abs(fc(pc.rma))>1)&tt(pc.rma)< 1e-4 >> > sigs<-featureNames(x.rma)[keep] >> > xmapConnect() > Select a database to connect to: > > 1: Hman ('xmapcore_homo_sapiens_58') > > Selection: 1 > password: > Warning message: > In .xmap.load.config() : > Environment 'R_XMAP_CONF_DIR' not set. Please refer to INSTALL.TXT for > information on how to set this up. > > Trying '.exonmap'. > >> > probeset.to.exon(sigs[1:5]) > *Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* >> > xmapConnect() > Select a database to connect to: > > 1: Hman ('xmapcore_homo_sapiens_58') > > Selection: 1 > >> > probeset.to.exon(sigs[1:5]) > Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist) > >> > xmap.connect() > password: > Disconnecting from xmapcore_homo_sapiens_58 (localhost) > Connected to xmapcore_homo_sapiens_58 (localhost) > Selected array 'HuEx-1_0' as a default. >> > probeset.to.exon(sigs[1:5]) > *Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_homo_sapiens_58.xmap_probesetToExon does not exist)* >> > sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-redhat-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] exon.pmcdf_1.1 exonmap_2.6.0 RColorBrewer_1.0-2 > genefilter_1.30.0 > [5] affy_1.26.1 Biobase_2.8.0 xmapcore_1.2.5 > digest_0.4.2 > [9] IRanges_1.6.8 RMySQL_0.7-4 DBI_0.2-5 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 > [4] preprocessCore_1.10.0 RSQLite_0.9-1 splines_2.11.0 > [7] survival_2.35-8 tcltk_2.11.0 tools_2.11.0 > [10] xtable_1.5-6 > > Regards, > > Anupam > -- > Graduate Student, > Center For DNA Fingerprinting And Diagnostics, > 4-1-714 to 725/2, Tuljaguda complex > Mozamzahi Road, Nampally, > Hyderabad-500001 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:15}}
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