[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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>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
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>>>>>       
>>>>>           
>>>   
>>>       
>
>
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