Dear Robert,

I eventually decided to create manually the featureData slot, since I  
got the following new error with getSnpAnnotation:

 > getSnpAnnotation(obj)
Error en sqliteExecStatement(con, statement, bind.data) :
   RS-DBI driver: (error in statement: String or BLOB exceeded size  
limit)

where the object "obj" is

oligoSnpSet (storageMode: lockedEnvironment)
assayData: 262264 features, 2 samples
   element names: calls, callsConfidence, cnConfidence, copyNumber
experimentData: use 'experimentData(object)'
Annotation: pd.mapping250k.nsp
phenoData
An object of class "AnnotatedDataFrame"
   sampleNames: Bf15418-Nsp, T15418-Nsp
   varLabels and varMetadata description:
     gender: male/female
     crlmmSNR: crlmmSNR
featureData
An object of class "AnnotatedDataFrame"
   featureNames: SNP_A-1780270, SNP_A-1780272, ..., SNP_A-4241299   
(262264 total)
   varLabels and varMetadata description: none
Annotation [1] "pd.mapping250k.nsp"

Then, I could use your function "hmm" on the first chromosome by using

 > obj.hmm = as(obj,"HmmSnpSet")
 > copyNumberIce(obj.hmm) <- FALSE
 > callsIce(obj.hmm) <- FALSE
 > chr=obj.hmm[chromosome(obj.hmm) %in% c(1),2]
 > chr.calls<-as(chr,"HmmSnpCallSet")

.. in order to analyze the LOH on this chromosome:

 > stateNames(chr.calls) <- c("loss", "ret")
 > pCHOM(chr.calls) <- c(0.999, 0.7)
 > initialStateProbability(chr.calls) <- c(1 - 0.99, 0.99)
 > predictions(chr.calls) <- matrix(NA, nrow(chr.calls),ncol(chr.calls))
 > callsIce(chr.calls)=FALSE
 > chr.hmm <- hmm(chr.calls)

[1] "Fitting HMM to chromosome 1"
[1] "   processing  p  arm of sample T15418-Nsp1.CEL  ..."
[1] "   processing  q  arm of sample T15418-Nsp1.CEL  ..."
 > breakpoints(chr.hmm)
           sampleId chromosome previous_SNP     start      last   
next_SNP       MB hiddenState     cytoband
6  T15418-Nsp           1     35079788  35130447  36608938  36650611  
1.478491        loss        p34.3
40 T15418-Nsp          1    188237023 188241377 189643292 189695104  
1.401915        loss        q31.2
38 T15418-Nsp          1    186945540 186977980 188003456 188030378  
1.025476        loss q31.1, q31.2
30 T15418-Nsp          1    151885390 151944721 152950730 153009199  
1.006009        loss          q22
8  T15418-Nsp          1     45383016  45408389  46381244  46554189  
0.972855        loss        p34.1
................

But, I obtain the following error with plotSnp:

 > plotSnp(chr.hmm)
Error en function (classes, fdef, mtable)  :
   unable to find an inherited method for function "plotSnp", for  
signature "HmmSnpCallSet", "missing"


Please, can you tell me whether this error is a bug or a error in my  
code.
Thank very much.
Please find bellow my sessionInfo()

R version 2.6.0 alpha (2007-09-05 r42787)
i386-apple-darwin8.10.1

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:
[1] VanillaICE_0.99.2           SNPchip_1.1.31               
pd.mapping250k.nsp_0.3.2
[4] oligo_1.1.17                oligoClasses_0.0.6           
affxparser_1.9.4
[7] AnnotationDbi_0.1.12        preprocessCore_0.99.12       
BufferedMatrixMethods_1.1.4
[10] BufferedMatrix_1.1.4        RSQLite_0.6-2               DBI_0.2-3
[13] affyio_1.5.11               Biobase_1.15.33

--  
________________________________________________________________________

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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