[BioC] ExonMap and xmap package question

[Zhu, Lihua (Julie)]

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
>