How to do comparision for tumors vs normal from different patients without taking average expression values using limma. How to find differentially expressed genes from 10 tumors and 5 normal from different patients?
Err, it'd be helpful if you clarified your experiment. Are the tumor/normal samples from the same patients (e.g., 5 patients each with 2 tumour biopsies and one normal tissue sample) or are these from 15 different patients? What is your objection to calculating group differences?
All 15 samples from different patients. Individual patient with one tumor.
Then you need to use an average, since the results are otherwise meaningless.
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