[BioC] Nonspecific filtering on Human Gene ST 1.0 Arrays
Javier Pérez Florido
jpflorido at gmail.com
Fri Nov 27 13:15:44 CET 2009
Martin Morgan escribió:
> "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".
>
I've checked that it only works when
annotation(subEset) <- "hugene10sttranscriptcluster"
Javier
> 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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>
>
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