[BioC] Human Gene ST using oligo package

[Mike Smith]

Hi Javier,

You can get a boxplot of the geneFeatureSet and expression set objects
using:

boxplot(log2(exprs(OligoRaw))) and boxplot(exprs(OligoEset)) respectively.

If I do the first command without the log transformation it takes about
10 minutes to plot for some reason, but it does still work.

Mike Smith


Javier Pérez Florido wrote:
> Dear Benilton,
> Thanks again for your help. Detaching 'affy' makes it work.
> However, I'm trying to use boxplot and histogram. For raw data it says:
>
> > boxplot(OligoRaw)
> Error in validObject(.Object) :
>   invalid class "ExpressionSet" object: featureNames differ between 
> assayData and featureData
> Error in exprs(channel(eset, chns[i])) :
>   error in evaluating the argument 'object' in selecting a method for 
> function 'exprs'
>
> And for an expression set object:
>
> > boxplot(OligoEset)
> Error in .local(x, ...) : object 'nsamples' not found
>
> Do I have to detach any other package?
>
> Thanks again,
> Javier
>
>
> > sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252    
> LC_MONETARY=Spanish_Spain.1252
> [4] LC_NUMERIC=C                   LC_TIME=Spanish_Spain.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] hugene10sttranscriptcluster.db_5.0.1 
> org.Hs.eg.db_2.4.1                   AnnotationDbi_1.10.0
>  [4] limma_3.4.0                          
> vsn_3.16.0                           genefilter_1.30.0
>  [7] pd.hugene.1.0.st.v1_3.0.1            
> RSQLite_0.8-4                        DBI_0.2-5
> [10] oligo_1.12.0                         
> oligoClasses_1.10.0                  Biobase_2.8.0
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.20.0     affy_1.26.0           affyio_1.16.0         
> annotate_1.26.0       Biostrings_2.16.0
>  [6] grid_2.11.0           IRanges_1.6.0         lattice_0.18-5        
> preprocessCore_1.10.0 splines_2.11.0
> [11] survival_2.35-8       tools_2.11.0          xtable_1.5-6
> >
>
>
> On 19/05/2010 21:56, Benilton Carvalho wrote:
>> detach affy and try again (when you loaded 'affy' you got a message
>> saying that oligo::probeNames was being masked).
>>
>> fyi: we do have ideas on how to solve this.
>>
>> b
>>
>> 2010/5/19 Javier Pérez Florido<jpflorido at gmail.com>:
>>   
>>> Dear list,
>>> Some time ago I used the oligo package to read and pre-process (rma) 
>>> a set
>>> of Human Gene ST 1.0 CEL files and it was OK.
>>>
>>> Now, I have resumed my work and with the new version of oligo and R 
>>> (below
>>> is my session info), the same code doesn't work (the new oligo 
>>> vignette is
>>> quite different to the one I used before). I have downloaded first the
>>> pd.hugene.1.0.st package from bioconductor and then I built it 
>>> myself (to
>>> check if it was a problem of the annotation package) and the same error
>>> appears:
>>>
>>> OligoRaw<-read.celfiles(filenames=list.celfiles())
>>> OligoEset<-rma(OligoRaw,target="core") # It is a GeneFeatureSet object
>>> Error in function (classes, fdef, mtable)  :
>>>   unable to find an inherited method for function "probeNames", for 
>>> signature
>>> "GeneFeatureSet"
>>>
>>> Any suggestions?
>>> Thanks,
>>> Javier
>>>
>>>
>>> R version 2.11.0 (2010-04-22)
>>> 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] grid      tools     tcltk     stats     graphics  grDevices utils
>>> datasets  methods   base
>>>
>>> other attached packages:
>>>   [1] hugene10sttranscriptcluster.db_5.0.1 org.Hs.eg.db_2.4.1
>>>    RColorBrewer_1.0-2
>>>   [4] gplots_2.7.4                         caTools_1.10
>>>    bitops_1.0-4.1
>>>   [7] gdata_2.8.0                          gtools_2.6.2
>>>    oneChannelGUI_1.14.2
>>> [10] RaExExonProbesetLocation_1.0.0       
>>> MoExExonProbesetLocation_1.0.0
>>>    HuExExonProbesetLocationHg19_0.0.2
>>> [13] edgeR_1.6.2                          IRanges_1.6.0
>>>     preprocessCore_1.10.0
>>> [16] GOstats_2.14.0                       graph_1.26.0
>>>    Category_2.14.0
>>> [19] AnnotationDbi_1.10.0                 tkWidgets_1.26.0
>>>    DynDoc_1.26.0
>>> [22] widgetTools_1.26.0                   affylmGUI_1.22.0
>>>    affyio_1.16.0
>>> [25] affy_1.26.0                          limma_3.4.0
>>>     pd.hugene.1.0.st.v1_0.0.1
>>> [28] pdInfoBuilder_1.12.0                 oligo_1.12.0
>>>    oligoClasses_1.10.0
>>> [31] affxparser_1.20.0                    RSQLite_0.8-4
>>>     DBI_0.2-5
>>> [34] Biobase_2.8.0
>>>
>>> loaded via a namespace:
>>>   [1] annotate_1.26.0   Biostrings_2.16.0 genefilter_1.30.0 GO.db_2.4.1
>>> GSEABase_1.10.0   RBGL_1.24.0       splines_2.11.0
>>>   [8] survival_2.35-8   XML_3.1-0         xtable_1.5-6
>>>
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>>>      
>>
>