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]]
> >
> > _______________________________________________
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> >
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