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

[Massimo Pinto]

That indeed solved the problem.

> annotation(esetPROC) <- "hgug4112a" # Very important. Must remove that .db from the name of the annotation package.
> esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=0.3) # cutoff at about the mean value xof my irqs

Thank you. I don't know how many weeks would have this taken without
the help from this list!
Massimo


On Fri, Oct 30, 2009 at 5:26 PM, Robert Gentleman <rgentlem at gmail.com> wrote:
> 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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>