Dear Prof Carey, dear Bioconductor user,

 Could you please tel me where can I find a clear tutorial on how creating
an smlSet class so I can use GGtools (I read the vignettes but still not
able to find clear information regarding snp data). For gene expression I
can create an eSet but how can I create SNP data slot from my genotype file.
I know That I should use snp.matrix but could we have an example (not based
on HapMap data).

also it would be useful to clarify regarding racExSet and smlist as this is
realy very confusing


I have 3 matrices:

gene expression (log2 scale)
               indiv1              indiv2    ...        indiv 1000

probe1       .....

probe2

probe 48,000  .....


SNP data
                       SNP1          SNP2         SNP 700,000
indiv1                  AA            AB               BB
indiv2
.....
indiv1000           .....            .......             ......

and pheno data

thanks for your help.


best regards,

Claire Pujoll, PhD

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