[BioC] Nonspecific filtering on Human Gene ST 1.0 Arrays
Martin Morgan
mtmorgan at fhcrc.org
Fri Nov 27 19:28:49 CET 2009
Hi Javier --
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.
Thanks for this. As Robert mentions, the intention is that nsFilter
should work whether or not the '.db' extension is present. Changes in
the last development cycle introduced bugs where this was not the case.
1.28.1 addressed this in one location, this is a second; version 1.28.2
should fix this when it becomes available, probably after noon (Seattle
time) tomorrow.
Martin
>
> 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 >
>>>>>> _______________________________________________
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>>>>>> Search the archives:
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>>>>>>
>>>>
>>
>>
>>
>
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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