[BioC] Problem with snprma

[OLIVIER NUÑEZ]

Dear Benilton,

I am trying to normalize a SNP type cell file with the oligo package.
But I obtain the following error with snprma:

> datos <- read.celfiles(list.celfiles())
Incompatible phenoData object. Created a new one.
Platform design info loaded.
> annotation(datos)
[1] "pd.mapping50k.hind240"
> preProc <- snprma(datos)
This may take a while.
Adjusting for sequence and fragment length......... done.
Normalizing...Error en sort(reference) : objeto "reference" no encontrado
Además: Warning messages:
1: there is no package called 'pd.mapping50k.hind240.crlmm.regions' in: 
library(package, lib.loc = lib.loc, character.only = TRUE, logical = 
TRUE,  2: data set 'pd.mapping50k.hind240Ref' not found in: data(list = 
paste(platform(oBatch), "Ref", sep = ""))

I had a glance to the function snprma() and I note that the default 
value for the "normalizeToHapmap" is TRUE and the reference object 
cannot be created.
Nevertheless, I guess that is not really the source of this error.
Please can help me to solve this problem.
best regards. Olivier

Bellow I attach my session Info
> sessionInfo()
R version 2.5.0 (2007-04-23) powerpc-apple-darwin8.9.1

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

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

other attached packages:
pd.mapping50k.hind240                 oligo BufferedMatrixMethods       
  BufferedMatrix               RSQLite                   DBI            
   "0.2.5"               "1.0.2"               "1.0.0"               
"1.0.0"               "0.5-4"               "0.2-3"               
affyio               Biobase              "1.4.0"              "1.14.0"



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________________________________________________________________________

Olivier G. Nuñez
nunez at est-econ.uc3m.es
Universidad Carlos III de Madrid        [ Tel : +34 663 03 69 09 ]
Departamento de Estadistica                [ Fax : +34 91 624 98 49 ]
Facultad de Ciencias Sociales
C/ Madrid 126 GETAFE 28903 SPAIN
Web Page: http://www.est-econ.uc3m.es/onunez

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-- 
________________________________________________________________________

Olivier G. Nuñez
nunez at est-econ.uc3m.es
Universidad Carlos III de Madrid        [ Tel : +34 663 03 69 09 ]
Departamento de Estadistica                [ Fax : +34 91 624 98 49 ]
Facultad de Ciencias Sociales
C/ Madrid 126 GETAFE 28903 SPAIN
Web Page: http://www.est-econ.uc3m.es/onunez