[BioC] Nonspecific filtering on Human Gene ST 1.0 Arrays

James W. MacDonald jmacdon at med.umich.edu
Tue Nov 24 17:58:47 CET 2009


Hi Javier,

Javier Pérez Florido wrote:
> 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

annotation(subEset) <- "hugene10sttranscriptcluster"

Should do the trick.

Best,

Jim


> 
> 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    >
> 
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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
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