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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