[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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