Xiayu,


1 metastasis sample won't reveal any honest statistics, unless you have
others the rule would be to ignore it.

Paired T-Test is the most sensitive measure. Use that if you have only 1
treatment (Tumor).
.
Good luck,
Michael


On Wed, Jun 26, 2013 at 10:47 AM, Rao,Xiayu <XRao@mdanderson.org> wrote:

> Hello,
>
>
>
> Thank you in advance for your help!
>
>
>
> I have 16 tumor samples and each one has a corresponding normal sample,
> which are 16 pairs. For one particular pair, there is a matched metastasis
> sample. When I analyzed the data using limma package and followed their
> protocol, is it right that I fit a linear model, and compare two contrasts
> of Tumor vs. Normal, and Metastasis vs. Normal? Or should I ignore that 1
> metastasis sample and just use paired ttest to test between Tumor and
> Normal?
>
>
>
> Best,
>
> Xiayu
>
>
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