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Dykema, Karl
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90
@dykema-karl-1116
Last seen 10.3 years ago
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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