[BioC] RNAither - problem with accessing biomaRt

Kishor Tappita kishor.tappita at gmail.com
Mon Aug 3 07:42:20 CEST 2009


Dear All,

When I am trying to perform mainAnalysis using RNAither. I get the
below error. Please help me in overcoming this issue.

Error in getBM(attributes = c("hgnc_symbol", goIDs), filters =
"hgnc_symbol",  :
  The query to the BioMart webservice returned an invalid result:
biomaRt expected a character string of length 1.
 Please report this to the mailing list.

Below is my sessionInfo
> sessionInfo()
R version 2.9.1 (2009-06-26)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets
methods   base

other attached packages:
 [1] biomaRt_2.0.0       RNAither_1.4.1      prada_1.20.0
rrcov_0.5-02
 [5] pcaPP_1.7           mvtnorm_0.9-7       robustbase_0.4-5
RColorBrewer_1.0-2
 [9] RankProd_2.16.0     topGO_1.12.0        SparseM_0.80
GO.db_2.2.11
[13] RSQLite_0.7-1       DBI_0.2-4           AnnotationDbi_1.6.1
Biobase_2.4.1
[17] graph_1.22.2

loaded via a namespace (and not attached):
 [1] annotate_1.22.0    geneplotter_1.22.0 lattice_0.17-25    limma_2.18.2
 [5] MASS_7.2-47        RCurl_0.98-1       stats4_2.9.1       tools_2.9.1
 [9] XML_2.5-1          xtable_1.5-5


Thanks,
Kishor



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