On Fri, Oct 29, 2010 at 12:14 PM, Sunny Srivastava
<research.baba@gmail.com>wrote:

> Hello Thomas,
> I am sure senior members of the list will have more to say, here is my
> $0.02.
>
> logFC is the coefficient of the treatment in your model. Assuming that you
> have a model with only one treatment
>
> log Int_g = b0 + b1 * trt
>
> b1 = logFC
>
> The CI of logFC can be found in the same manner as you would do in normal
> linear regression, but here instead of usual t(0.975, df) quantile, you
> should use the moderated t quantile ie t(0.975, df.residual + df.prior)
>
> So the 95% CI for logFC will be
>
> logFC -+ t(0.975, fit3$df.residual + fit3$df.prior) * fit3$stdev.unscaled *
> sqrt(fit3$s2.post)
>
>
> Please correct me if I am wrong.
>
>
> Thanks,
> S.
>

Hi Sunny:

sorry for the very late reply.
Is fit3 the return value from eBayes()?

Timothy

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