Dear Benilton, thanks for your help!
When I try your code, I get this error:

Error in as.hi.integer(x, maxindex = maxindex, dim = dim, vw = vw, pack =
pack) :
  NAs in as.hi.integer
In addition: Warning message:
In `[<-.ff_array`(`*tmp*`, theCalls == i, value = "AA") :
  opening ff
C:/Users/Pina/Bioinformatica/SNP/COR354_SNP6/call-9201fc1496a.ff

And then when I use write.table function I get this error:

Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors =
stringsAsFactors) :
  cannot coerce class 'c("ff_matrix", "ff_array", "ff")' into a data.frame

Can you help me? thanks a lot!
Pina
2012/7/13 Benilton Carvalho <beniltoncarvalho@gmail.com>

> there is a calls() accessor that will return you the calls as integers
> (1: AA; 2: AB; 3: BB). So, something along the lines of:
>
> theCalls = calls(object)
> final = theCalls
> for (i in 1:3)
>    final[theCalls == i] = c('AA', 'AB', 'BB')[i]
>
> Then it's just a matter of using write.table() to write out the file
> using the "final" object.
>
> b
>
> On 13 July 2012 11:22, Pina Iannelli <pina.iannelli@gmail.com> wrote:
> > Dear all,
> > I run this code to get genotyping from Affymetrix SNP 6.0 arrays:
> >
> > fullFilenames <-
> > list.celfiles("C:/Users/Pina/Bioinformatica/SNP/COR354_SNP6", full.names
> =
> > TRUE)
> > outputDir <- file.path(getwd(), "crlmmResults")
> > exampleSet <- genotype(fullFilenames, batch = rep("1", 2), cdfName =
> > "genomewidesnp6", gender=c(1, 2))
> >
> > Now I nead to ha ve a file with genotyping information, such as:
> >
> >    SNP_A-1780270 BB BB AA  SNP_A-1780272 BB AB BB
> > How can I do it?
> > Thanks for your help, best regards
> > Pina
> >
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> >
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