exonmap package - MySQL error
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Dykema, Karl ▴ 90
Last seen 8.4 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 This email message, including any attachments, is for th...{{dropped:6}}
exonmap exonmap • 649 views

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