[BioC] Nonspecific filtering on Human Gene ST 1.0 Arrays

[cstrato]

Dear Javier,

It might be of interest to you that package xps could handle your 
problem of removing different control genes, since function rma() has a 
parameter "exonlevel" for HuGene and HuExon arrays, which allows you to 
define which probesets to use for rma, e.g. exonlevel="affx+core" will 
use only probesets of category 'unique', 'similar' and 'mixed' plus the 
standard AFFX controls, while exonlevel="metacore" will only use 
probesets of category 'unique', see the help "?exonLevel". Thus there is 
no need to remove these probesets afterwards. Furthermore, xps has also 
different methods for non-specific filtering, see help "?PreFilter"

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._


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"
>
> 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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