[BioC] Human Gene ST using oligo package

[Javier Pérez Florido]

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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>      
>