[BioC] Nonspecific filtering on Human Gene ST 1.0 Arrays
Javier Pérez Florido
jpflorido at gmail.com
Fri Nov 27 16:51:36 CET 2009
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 >
>>>>> _______________________________________________
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>>>>>
>>>>>
>>>
>>>
>
>
>
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