I am wondering how to compare two separate groups that each contain paired tumor normal samples, so assuming we have this experimental setup:
Sample 1_normal good_outcome Sample 1_tumor good_outcome Sample 2_normal good_outcome Sample 2_tumor good_outcome Sample 3_normal bad_outcome Sample 3_tumor bad_outcome Sample 4_normal bad_outcome Sample 4_tumor bad_outcome
is there a way to compare the tumor samples of both groups, taking into account the paired normal samples? My first guess would have been a paired t-test, however, since this is not a before-after comparison I am not sure if it can be applied. To clarify, we have RNA-seq samples with this setup available and I would to use egedR or voom/limma to do this comparison, but I do not know how to create an appropriate contrast matrix (if this is even possible).
Any help is greatly appreciated.