[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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