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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?
