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 Adem?s: 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. Nu?ez 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. Nu?ez 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

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 NU?EZ 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 > Adem?s: 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. Nu?ez > 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. Nu?ez > 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