Dear Olivier,

See Section 3.3 of the vignette.  In particular, note that you will  
need to install the callsConfidence package available here:

http://www.biostat.jhsph.edu/~rscharpf/software/index.html

So try that first and then let me know if you still get an error.   
I've added a line in VanillaICE that checks to see whether this is  
installed (version 0.99.5).  Because callsConfidence is not yet in  
Bioconductor, its a bit harder to write code in VanillaICE that  
checks for bugs with the ICE HMM -- so comments/suggestions welcome.

In the next release of Bioconductor (2.2),  we'll add callsConfidence  
to the experiment data repository and we'll change the names required  
in the annotation slot to the corresponding names of the annotation  
packages in Bioconductor.

Best regards,

Rob

> 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] RColorBrewer_1.0-1       VanillaICE_0.99.2         
> SNPchip_1.1.32           R.utils_0.9.6
> [5] R.oo_1.3.0               pd.mapping250k.nsp_0.3.2  
> oligo_1.1.22             oligoClasses_0.99.2
> [9] affxparser_1.9.5         AnnotationDbi_0.1.15      
> preprocessCore_0.99.17   RSQLite_0.6-2
> [13] DBI_0.2-3                Biobase_1.15.33
>
> loaded via a namespace (and not attached):
> [1] affyio_1.5.11


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