[BioC] Nonspecific filtering on Human Gene ST 1.0 Arrays
Robert Gentleman
rgentlem at fhcrc.org
Fri Nov 27 17:30:43 CET 2009
Hi,
Benilton Carvalho wrote:
> This is possibly due to my email about one week ago when I suggested that:
>
> annotation(OligoEset) <- "hugene10sttranscriptcluster.db"
>
> would suffice. But apparently the ".db" bit isn't required.
it should not be. It is essentially conveying an implementation
detail (that this annotation package is stored as a database), clearly
other implementations (like our old environment based one should also
work, if one wanted to use them). So my preference is that the .db not
be required.
best wishes
Robert
>
> b
>
> On Nov 27, 2009, at 1:51 PM, Javier Pérez Florido wrote:
>
>> Martin Morgan escribió:
>>> Javier Pérez Florido wrote:
>>>
>>>> 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"
>>>>
>>>
>>> Can you be more specific? The previous error was
>>>
>>>
>>>>>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) :
>>>>>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found
>>>>>>>
>>>
>>> if you see the same message then can you confirm that you have
>>> genefilter 1.28.1 installed? If there is a different error then can you
>>> please provide me with that? I do not have a 'real' hugene eset with
>>> which to work.
>>>
>>> Martin
>>>
>> Dear Martin,
>> I've updated genefilter from version 1.28.0 to version 1.28.1. When I'm
>> trying to use genefilter
>>
>> annotation(OligoEset) <- "hugene10sttranscriptcluster.db"
>> OligoEset<-nsFilter(OligoEset, require.entrez=TRUE,require.GOBP=TRUE,
>> remove.dupEntrez=TRUE,
>> var.func=IQR,var.cutoff=varCutoff,filterByQuantile=TRUE,
>> feature.exclude="petete")$eset
>> Error in get(paste(data, centID, sep = "")) :
>> object 'hugene10sttranscriptcluster.dbENTREZID' not found
>>
>> However, if
>> annotation(OligoEset) <- "hugene10sttranscriptcluster"
>>
>> nsFilter works well.
>>
>> Hope this helps,
>> Javier
>>
>> R version 2.10.0 (2009-10-26)
>> i386-pc-mingw32
>>
>> locale:
>> [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
>> 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] pd.hugene.1.0.st.v1_3.0.0
>> oligo_1.10.0 preprocessCore_1.8.0
>> [4] oligoClasses_1.8.0
>> genefilter_1.28.1 GOstats_2.12.0
>> [7] graph_1.24.0
>> Category_2.12.0 limma_3.2.1
>> [10] hugene10sttranscriptcluster.db_4.0.1
>> org.Hs.eg.db_2.3.6 RSQLite_0.7-3
>> [13] DBI_0.2-4
>> AnnotationDbi_1.8.0 vsn_3.14.0
>> [16] Biobase_2.6.0
>>
>> loaded via a namespace (and not attached):
>> [1] affxparser_1.18.0 affy_1.24.0 affyio_1.14.0
>> annotate_1.24.0 Biostrings_2.14.0 GO.db_2.3.5 grid_2.10.0
>> [8] GSEABase_1.8.0 IRanges_1.4.0 lattice_0.17-26
>> RBGL_1.20.0 splines_2.10.0 survival_2.35-7 tools_2.10.0
>> [15] XML_2.6-0 xtable_1.5-5
>>>
>>>> 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 >
>>>>>>> _______________________________________________
>>>>>>> Bioconductor mailing list
>>>>>>> Bioconductor at stat.math.ethz.ch
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>> Search the archives:
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>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>
>>>
>>>
>>
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>
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