[BioC] error while using genefilter's nsFilter: could not find function "hgug4112a.db_dbconn"

[Robert Gentleman]

Hi

Robert Gentleman

On Oct 30, 2009, at 7:11 AM, Massimo Pinto <pintarello at gmail.com> wrote:

> 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"
>

This is probably part of the problem
Drop the .db suffix it is not part of the annotation.
You should Use "hgug4112a"


> 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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