I want to test for significance between differences in cell count between conditions.
I have 2 conditions (N, T), 3 donors (samples) each, and four cell types (A-D) as shown in the example below.
I believe this problem is analogous to the differential expression test performed with edgeR or DEseq.
Example data:
Count Sample Celltype Condition
555 P1 D T
3829 P1 C T
945 P1 A T
222 P1 B T
795 P2 D T
5464 P2 C T
839 P2 A T
438 P2 B T
629 P3 D T
6426 P3 C T
647 P3 A T
457 P3 B T
8 P1 D N
5122 P1 C N
3204 P1 A N
1 P1 B N
20 P2 D N
6111 P2 C N
2524 P2 A N
26 P2 B N
66 P3 D N
7490 P3 C N
5272 P3 A N
3 P3 B N