I have RNA-seq from two sequencing batches; Lab technician says that he has run the RNA expression quantification two times in bathes 1 and 2 for example tumor 1 in batch 1 and tumor 1 in batch 2 , normal 2 in batch1 and normal 2 in batch 2. PCA shows however shows two experimental runs are too close to each other and can be merged
[![enter image description here][1]][1]
Now my question is can I compare only a tumour sample with its own matched normal sample in one patient
to get differentially expressed genes for this patient
by using experimental runs (technical replicates )? Design would be Tumour1_batch1
Tumour1_batch2
versus Normal1_batch1
Normal1_bacth2
> head(mycols)
Condition
Normal1_batch1 N
Normal1_batch2 N
Tumour1_batch1 T
Tumour1_batch2 T
sd
andvar
). However, how generalizable it would be ? What is your biological question behind this comparison? One thing is to pair the samples and control for batch effect and another is to just compare 4 samples. $\endgroup$