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I am comparing three groups A, B and C and they are in 3 batches of library preparation. In the
Sample Name | Condition | Batch |
---|---|---|
1 | A | 1 |
2 | A | 1 |
3 | B | 1 |
4 | B | 1 |
5 | A | 2 |
6 | A | 2 |
7 | B | 2 |
8 | B | 2 |
9 | C | 3 |
10 | C | 3 |
11 | B | 3 |
12 | B | 3 |
Is the group C being in only batch 3 confounding or can I use the condition B to correct the batch effect in all batches and successfully compare A and C?