I have two matrices, one for individuals before treatment and one for the same individuals after treatment. Both matrices are raw read counts of RNA expression.
Treated_1 Treated_2 Treated_3 Treated_4 Treated_5
RNA_1 105 283 64 155 51
RNA_2 359 27 47 348 84
RNA_3 99 10 89 345 77
RNA_4 48 100 77 74 83
Untreated_1 Untreated_2 Untreated_3 Untreated_4 Untreated_5
RNA_1 100 200 50 130 33
RNA_2 200 10 30 300 75
RNA_3 90 10 60 320 60
RNA_4 66 50 33 60 55
How can I tell which RNA's are significantly differentially expressed in R using edgeR
or DESeq2
? I'm thinking first normalize using TMM then compare the mean of the normalized values for treated vs. untreated?