Hi benilton,

I  actually got the pd.mapping50k.hind240 by Vince Carey (version 2.5  
as given in my session info, see my previous message).

The command  dir(system.file("extdata",  
package="pd.mapping50k.hind240"))

[1] "pd.mapping50k.hind240.spline.params.rda"  
"pd.mapping50k.hind240.sqlite"
[3] "pd.mapping50k.hind240CrlmmInfo.rda"       
"pd.mapping50k.hind240Ref.rda"
[5] "seqMat.rda"

Thanks. Olivier
--  
________________________________________________________________________

Olivier G. Nuñez
nunez@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

________________________________________________________________________


El 24/05/2007, a las 17:04, Benilton Carvalho escribió:

> Hi Olivier,
>
> did you get pd.mapping50k.hind240 from:
>
> http://bioconductor.org/packages/2.0/data/annotation/html/ 
> pd.mapping50k.hind240.html
>
> what do you get if you:
>
> dir(system.file("extdata", package="pd.mapping50k.hind240"))
>
> thanks,
>
> b
>
> On May 24, 2007, at 10:53 AM, OLIVIER NUÑEZ wrote:
>
>> 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"
>>
>>
>>
>> --
>>
>> --
>> _____________________________________________________________________ 
>> ___
>>
>> Olivier G. Nuñez
>> nunez@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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