[BioC] exonmap/xmapcore error

[James W. MacDonald]

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
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