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

[James W. MacDonald]

Hi Massimo,

Massimo Pinto 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"

This could probably use a better error message. The problem is that you 
don't have the annotation package for this chip available, so you cannot 
  filter based on things like Entrez Gene, GO BP, etc.

I assume this is a custom chip, so you will need to get the annotation 
file from Affy and build an annotation package yourself using SQLForge. 
See the SQLForge vignette for more information:

http://www.bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/inst/doc/SQLForge.pdf

Best,

Jim


> 
>> 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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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826