[BioC] exonmap package - MySQL error

[Dykema, Karl]

Bioc users -

I am trying to set up the exonmap package and I have run into a problem that does not appear to be previously discussed in the mailing list. I have installed my local copy of Ensembl as well as the X-map database, as shown here. I can load exonmap library and the example data but I run into a MySQL error when I try to connect to the database. I am quite certain that I am connecting to the database because I was previously getting a different error message about user permissions. Can anyone offer any suggestions? Session info also included below. Thanks a lot.



mysql> use homo_sapiens_core_45_36g
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+---------------------------------------+
| Tables_in_homo_sapiens_core_45_36g    |
+---------------------------------------+
| alt_allele                            |
| analysis                              |
| analysis_description                  |
| array                                 |
| arrayset                              |
| assembly                              |
| assembly_exception                    |
[...]





> data(exonmap)
> pc.exonmap <- pc(x.rma,"group",c("a","b"))
> sigs <- names(fc(pc.exonmap))[abs(fc(pc.exonmap)) > 1 & tt(pc.exonmap) < 1e-04]
> length(sigs)
[1] 31
> xmapDatabase("Human")
done.
Warning message:
In .dbSetup("human.mycnf") :
  Don't know where configuration files are: environment variable R_XMAP_CONF_DIR is not set. trying '~/.exonmap'.
> sig.exons <- probeset.to.exon(sigs)
> length(sig.exons)
[1] 21
> probeset.to.transcript(sigs)
 [1] "ENST00000260128" "ENST00000373050" "ENST00000373051" "ENST00000230321"
 [5] "ENST00000343101" "ENST00000380423" "ENST00000291525" "ENST00000367928"
 [9] "ENST00000381572" "ENST00000337976" "ENST00000263463" "ENST00000325455"
[13] "ENST00000309109"
> select.probewise(sigs,filter="exonic")
Error in mysqlExecStatement(conn, statement, ...) :
  RS-DBI driver: (could not run statement: Column 'probeset_id' in field list is ambiguous)






> sessionInfo()
R version 2.6.0 (2007-10-03)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] exonmap_1.2.02       plier_1.8.0          RMySQL_0.6-0
 [4] DBI_0.2-4            RColorBrewer_1.0-2   simpleaffy_2.14.05
 [7] gcrma_2.10.0         matchprobes_1.10.0   genefilter_1.16.0
[10] survival_2.32        affy_1.16.0          preprocessCore_1.0.0
[13] affyio_1.6.1         Biobase_1.16.1

loaded via a namespace (and not attached):
[1] annotate_1.16.0     AnnotationDbi_1.0.6 rcompgen_0.1-15
[4] RSQLite_0.6-3



-----------------------------------------
Karl Dykema
Lab of Computational Biology
Van Andel Research Institute
333 Bostwick Ave NE
Grand Rapids, MI 49503
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