[BioC] qc in simpleaffy

[Mayte Suarez-Farinas]

Hi all!


I try what it was suggested from my previous post. But now I get  
another error:
I load only the minimum libraries: here is what i got:

  library(simpleaffy)
  load("Batch1-AffyBatch.rda")
  qcs<-qc(abatch)
  plot(qcs)
Error in as.double(y) :
   cannot coerce type 'S4' to vector of type 'double'

so, whats teh problem now??



sessionInfo()
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils      
datasets  methods   base

other attached packages:
  [1] hgu133a2.db_2.2.5    RSQLite_0.7-1        DBI_0.2-4             
AnnotationDbi_1.5.18 hgu133plus2cdf_2.3.0
  [6] simpleaffy_2.18.0    gcrma_2.14.1         matchprobes_1.14.1    
genefilter_1.22.0    survival_2.34-1
[11] affy_1.20.2          Biobase_2.2.2

loaded via a namespace (and not attached):
[1] affyio_1.10.1        annotate_1.20.1      preprocessCore_1.4.0




On Apr 23, 2009, at 6:59 PM, Chao-Jen Wong wrote:

> Hi, Mayte,
>
> Can you try typing Biobase::annotation(abatch) and see if it still  
> gives
> any error. If not, then that means the "annotation" method may be
> crushed by other packages in your search path. It seems to me that you
> upload a lot of packages into the workspace.  Can you try to leave  
> the R
> environment and call up R again. Don't load too many libraries this
> time, only affy and simpleaffy and your affyBatch data object.  Hope
> that would work.
>
> Chao-Jen
>
> Mayte Suarez-Farinas wrote:
>> Hi everybody:
>>
>> I am working with R 2.8 and I the function "qc" from simpleaffy is  
>> not
>> working:
>>
>>> q<-qc(abatch)
>> Error in function (classes, fdef, mtable)  :
>>   unable to find an inherited method for function "annotation", for
>> signature "AffyBatch"
>>
>> I get the same error if:
>>
>>> annotation(abatch)
>> Error in function (classes, fdef, mtable)  :
>>   unable to find an inherited method for function "annotation", for
>> signature "AffyBatch"
>>
>> but not if:
>>
>>> abatch at annotation
>> [1] "hgu133a2.db"
>>
>>
>> sessionInfo()
>> R version 2.8.1 (2008-12-22)
>> i386-apple-darwin8.11.1
>>
>> locale:
>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils
>> datasets  methods   base
>>
>> other attached packages:
>>  [1] hgu133plus2probe_2.3.0 hgu133plus2cdf_2.3.0
>> Harshlight_1.12.0      altcdfenvs_2.4.0
>>  [5] hypergraph_1.14.0      Biostrings_2.10.16
>> IRanges_1.0.12         makecdfenv_1.20.0
>>  [9] affyio_1.10.1          beadarray_1.10.0
>> sma_0.5.15             hwriter_1.0
>> [13] affycoretools_1.14.1   annaffy_1.14.0
>> KEGG.db_2.2.5          biomaRt_1.16.0
>> [17] GOstats_2.8.0          Category_2.8.4
>> RBGL_1.18.0            GO.db_2.2.5
>> [21] RSQLite_0.7-1          DBI_0.2-4
>> graph_1.20.0           limma_2.16.4
>> [25] affyQCReport_1.20.0    geneplotter_1.20.0
>> annotate_1.20.1        AnnotationDbi_1.5.18
>> [29] lattice_0.17-17        RColorBrewer_1.0-2
>> affyPLM_1.18.1         preprocessCore_1.4.0
>> [33] xtable_1.5-4           simpleaffy_2.18.0
>> gcrma_2.14.1           matchprobes_1.14.1
>> [37] genefilter_1.22.0      survival_2.34-1
>> affy_1.20.2            Biobase_2.2.2
>>
>> loaded via a namespace (and not attached):
>> [1] GSEABase_1.4.0     KernSmooth_2.22-22 Matrix_0.999375-21
>> RCurl_0.94-1       XML_2.1-0
>> [6] cluster_1.11.11    grid_2.8.1
>>
>> _______________________________________________
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>
>
> -- 
> Chao-Jen Wong
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Avenue N., M2-B876
> PO Box 19024
> Seattle, WA 98109
> 206.667.4485
> cwon2 at fhcrc.org
>