[BioC] error while using genefilter's nsFilter: could not find function "hgug4112a.db_dbconn"
Massimo Pinto
pintarello at gmail.com
Fri Oct 30 12:11:13 CET 2009
Greetings all,
I have finally come across to genefilter's nsFIlter(); it looks like
it's going to do quite a lot for me in just one call. I called it as
follows:
> esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=0.5)
Error in do.call(paste(chip, "_dbconn", sep = ""), list()) :
could not find function "hgug4112a.db_dbconn"
> annotation(esetPROC)
[1] "hgug4112a.db"
here's some info on my session:
> sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-apple-darwin9.8.0
locale:
[1] C
attached base packages:
[1] grid tcltk stats graphics grDevices utils
datasets methods base
other attached packages:
[1] affy_1.24.0 gplots_2.7.3 caTools_1.10
bitops_1.0-4.1 gdata_2.6.1 gtools_2.6.1
[7] hgug4112a.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3
DBI_0.2-4 Agi4x44PreProcess_1.5.1
genefilter_1.28.0
[13] annotate_1.24.0 AnnotationDbi_1.7.20 limma_3.2.1
Biobase_2.6.0
loaded via a namespace (and not attached):
[1] affyio_1.13.5 preprocessCore_1.7.9 splines_2.10.0
survival_2.35-7 tools_2.10.0 xtable_1.5-5
Thanks a lot,
Yours
Massimo
Massimo Pinto
Post Doctoral Research Fellow
Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome
http://claimid.com/massimopinto
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