[BioC] Problem with snprma

[Benilton Carvalho]

Dear Olivier,

http://www.biostat.jhsph.edu/~bcarvalh/oligo_1.0.2-1.tar.gz

addresses this problem. Could you please give it a try and let me  
know if everything ran as expected?

thank you,

b

On May 24, 2007, at 11:24 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 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
>
> ______________________________________________________________________ 
> __
>
>
> ----- Terminar mensaje reenviado -----
>
>
> --
>
> --
> ______________________________________________________________________ 
> __
>
> 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
>
> ______________________________________________________________________ 
> __



--
Benilton Carvalho
PhD Candidate
Department of Biostatistics
Bloomberg School of Public Health
Johns Hopkins University
bcarvalh at jhsph.edu