I've a small question concerning differential expression analysis regarding 12 samples divided into 2 cell lines (cell 1 & 2), two conditions: tumor (T) and control (C):
|Cell||Condition||Patient number (p)|
In order to capture the differences among Cell1 and Cell2 (considering Cell2 and condition C as reference levels), I used the following model:
design = ~ Cell+Condition+Cell:Condition
but the DEGs (significant genes) I am getting here via interaction term (Cell:Condition) is not considering patient. Therefore, please help me to design a model which can perform a differential expression analysis by doing the following:
(i) Cell1/Cell2: T samples vs. Cell1/Cell2 C samples including patient information.
I like to obtain DEGs between Cell 1 and Cell2 cell lines considering (i) comparison.