On Tue, Dec 18, 2012 at 2:14 PM, zhengyu jiang <zhyjiang2006@gmail.com>wrote:

> Hi Sean,
> Thanks for the quick response.  I have both for the same sample but I am
> interested in expresssion analysis. Should I sum up all the SNP reads?
>
>
I'm not sure what you mean by "SNP reads".  However, you might want to look
at the GGtools package for looking into eQTL analysis which is, it seems,
what you are interested in doing.

Sean



> Jiang
>
> On Tue, Dec 18, 2012 at 2:08 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
> >
> >
> > On Tue, Dec 18, 2012 at 1:57 PM, zhengyu jiang <zhyjiang2006@gmail.com
> >wrote:
> >
> >> Hi there,
> >>
> >> I am trying to deal with SNPs in the two channel
> >> beadchip microarray expression analysis. Does anyone know how
> >> to calculate the expression of some genes with SNPs (heterozygotes or
> >> homozygotes)? Is there any package for this?
> >> This is probably an old question but I cannot find the answer from
> google.
> >>
> >
> > Hi, Jiang.
> >
> > Could you clarify what data types you have?  Do you have SNP/genotype
> > data?  Do you have gene expression data?  Are these data on the same
> > samples?
> >
> > Sean
> >
> >
>
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