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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