Dear Claire,

If you are seeing references to racExSet, you are looking at an outdated
version of the GGtools package.  The GGBase package includes a function
make_smlSet that helps create the structure.  As you note, the snpMatrix
package defines the snp.matrix class.  The snpMatrix package has functions
that generate snp.matrix instances from ped format, hapmap-formatted data,
plink-formatted data, or chiamo-formatted data.  If you do not use any of
these formats, you will have to create a list of snp.matrix objects, each
element created according to specifications in the snpMatrix package.

If you have up-to-date versions of the software and would like further
guidance, provide a small excerpt of your genotyping data file and I will
provide illustration of how to create the associated smlSet, using some
dummy expression and phenotype data.  Clearly the most convenient approach
will be based on a conventional format for genotyping data such as those
enumerated above.

On Wed, Mar 31, 2010 at 8:29 PM, claire pujoll <cpujoll@gmail.com> wrote:

> 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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