2009/11/24 Javier Pérez Florido <jpflorido@gmail.com>

> 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
>

The reason for this error is that the defaults include things like
require.entrez=TRUE, which would require an ability to map probes to entrez
genes.  if you set require.entrez and remove.dupEntrez to FALSE,
it should work.


>
> 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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