[BioC] barcode with custom CDF

Dario Greco [guest] guest at bioconductor.org
Tue Mar 26 12:03:15 CET 2013

Dear BioC-ers,

I would like to run the function 'barcode' on a set of CEL files preprocessed with a custom CDF.
I am wondering if there is a quick way to generate the needed vectors (mu and tau for the unexpressed distribution) in the same way as the package frmaTools allows for the fRMA necessary vectors.
I hope I am not posting about an issue already treated in this mailing list, but searching it produced no obvious hints.

thanks a lot for your help and suggestions.

 -- output of sessionInfo(): 

R version 2.15.3 (2013-03-01)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] hgu133plus2barcodevecs_1.0.5 hgu133plus2frmavecs_1.1.12  
 [3] hgu133abarcodevecs_1.0.5     hthgu133acdf_2.11.0         
 [5] AnnotationDbi_1.20.7         affy_1.36.1                 
 [7] frma_1.10.0                  Biobase_2.18.0              
 [9] BiocGenerics_0.4.0           BiocInstaller_1.8.3         

loaded via a namespace (and not attached):
 [1] affxparser_1.30.2     affyio_1.26.0         Biostrings_2.26.3    
 [4] bit_1.1-10            codetools_0.2-8       DBI_0.2-5            
 [7] ff_2.2-11             foreach_1.4.0         GenomicRanges_1.10.7 
[10] IRanges_1.16.6        iterators_1.0.6       MASS_7.3-23          
[13] oligo_1.22.0          oligoClasses_1.20.0   parallel_2.15.3      
[16] preprocessCore_1.20.0 RSQLite_0.11.2        splines_2.15.3       
[19] stats4_2.15.3         tools_2.15.3          zlibbioc_1.4.0       

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