[BioC] exonmap/xmapcore error
Paul Leo
p.leo at uq.edu.au
Wed Jul 21 01:57:51 CEST 2010
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 at 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
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