ExonMap and xmap package question
1
0
Entering edit mode
Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 5 months ago
United States
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
probe limma convert exonmap probe limma convert exonmap • 667 views
ADD COMMENT
0
Entering edit mode
Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 5 months ago
United States
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 >
ADD COMMENT

Login before adding your answer.

Traffic: 315 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6