Hi, I am trying to analyze mouse exon array moex10stv1 using exonMap and xmap. I have downloaded xmapcore_mus_musculus_60.tar.gz from http://xmap.picr.man.ac.uk/download#mmxmapcore,set up a local mysql database and environment as instructed. After obtaining a list of probes that are significant using limma, I ran the following exonMap functions to convert the probe ID to exon ID and transcript ID, but encountered following errors. ##### connection is successful xmapConnect("mouse") ### sigs are a list of probes sig.exons <- probeset.to.exon(sigs) Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: PROCEDURE xmapcore_mus_musculus_60.xmap_probesetToExon does not exist) sig.transcripts <- probeset.to.transcript(sigs) Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: PROCEDURE xmapcore_mus_musculus_60.xmap_probesetToTranscript does not exist) Looks like the mapping tables are missing. If that is the issue, where should I download the missing mapping tables? Thank you very much for your help! Best regards, Julie sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] xmapcore_1.2.8 digest_0.4.2 IRanges_1.6.11 [4] limma_3.4.4 mouseexonpmcdf_1.9.1 exonmap_2.6.1 [7] RMySQL_0.7-5 DBI_0.2-5 RColorBrewer_1.0-2 [10] genefilter_1.30.0 affy_1.26.1 Biobase_2.8.0 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_0.9-2 splines_2.11.1 [7] survival_2.35-8 tools_2.11.1 xtable_1.5-6

It turns out that ExonMap has been deprecated. Now I am using xmapcore and it works so far. Thanks so much for such a useful package! Best regards, Julie On 12/8/10 1:46 PM, "Julie Zhu" <julie.zhu at="" umassmed.edu=""> wrote: > Hi, > > I am trying to analyze mouse exon array moex10stv1 using exonMap and xmap. > > I have downloaded xmapcore_mus_musculus_60.tar.gz from > http://xmap.picr.man.ac.uk/download#mmxmapcore,set up a local mysql database > and environment as instructed. > > After obtaining a list of probes that are significant using limma, I ran the > following exonMap functions to convert the probe ID to exon ID and > transcript ID, but encountered following errors. > > ##### connection is successful > xmapConnect("mouse") > ### sigs are a list of probes > sig.exons <- probeset.to.exon(sigs) > Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_mus_musculus_60.xmap_probesetToExon does not exist) > sig.transcripts <- probeset.to.transcript(sigs) > Error in mysqlExecStatement(conn, statement, ...) : > RS-DBI driver: (could not run statement: PROCEDURE > xmapcore_mus_musculus_60.xmap_probesetToTranscript does not exist) > > Looks like the mapping tables are missing. If that is the issue, where > should I download the missing mapping tables? > > Thank you very much for your help! > > Best regards, > > Julie > > sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xmapcore_1.2.8 digest_0.4.2 IRanges_1.6.11 > [4] limma_3.4.4 mouseexonpmcdf_1.9.1 exonmap_2.6.1 > [7] RMySQL_0.7-5 DBI_0.2-5 RColorBrewer_1.0-2 > [10] genefilter_1.30.0 affy_1.26.1 Biobase_2.8.0 > > 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_0.9-2 splines_2.11.1 > [7] survival_2.35-8 tools_2.11.1 xtable_1.5-6 >