[BioC] Nonspecific filtering on Human Gene ST 1.0 Arrays

[Martin Morgan]

"James W. MacDonald" <jmacdon at med.umich.edu> writes:

> 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"

genefilter 1.28.1 should work for both
"hugene10sttranscriptcluster.db" and "hugene10sttranscriptcluster".

Martin

> 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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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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