[BioC] Nonspecific filtering on Human Gene ST 1.0 Arrays

[Javier Pérez Florido]

Dear list,
I've tried to use the nsFilter function from genefilter package to 
perform nonspecific filtering on a Human Gene ST 1.0 dataset.
The expression set has the hugene10sttranscriptcluster.db annotation 
package, but when nsFilter is applied:

nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those without 
EntrezGene IDs, etc
Error is do.call(paste(chip, "_dbconn", sep = ""), list()) :
 "hugene10sttranscriptcluster.db_dbconn" cannot be found

Maybe nsFilter is not built for this kind of microarrays, although 
varFilter,from the same package, works, because it makes use of the 
expression values only.

I've made some search on Google, but no success. I can write a function 
that removes the different control genes in Human Gene (AFFX, spike, 
neg_control,pos_control,etc) and those without EntrezGene ID, but wanted 
to know if there is a function that handle this for this kind of 
microarrays.

Thanks,
Javier


sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32

locale:
[1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252  
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C                 
[5] LC_TIME=Spanish_Spain.1252   

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

other attached packages:
 [1] Matrix_0.999375-31                   
lattice_0.17-26                    
 [3] ALL_1.4.7                            
genefilter_1.28.0                  
 [5] pd.hugene.1.0.st.v1_3.0.0            
Category_2.12.0                    
 [7] KEGG.db_2.3.5                        
hugene10sttranscriptcluster.db_4.0.1
 [9] org.Hs.eg.db_2.3.6                   
RSQLite_0.7-3                      
[11] DBI_0.2-4                            
oligo_1.10.0                       
[13] preprocessCore_1.8.0                 
oligoClasses_1.8.0                 
[15] GSEABase_1.8.0                       
graph_1.24.0                       
[17] annotate_1.24.0                      
AnnotationDbi_1.8.0                
[19] Biobase_2.6.0                      

loaded via a namespace (and not attached):
 [1] affxparser_1.18.0 affyio_1.14.0     Biostrings_2.14.0 grid_2.10.0     
 [5] IRanges_1.4.0     RBGL_1.20.0       splines_2.10.0    survival_2.35-7 
 [9] tools_2.10.0      XML_2.6-0         xtable_1.5-5    
 >