[BioC] ExonMap and xmap package question

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Wed Dec 8 19:46:30 CET 2010


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
### 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,


R version 2.11.1 (2010-05-31)

[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  

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