In a 3 group DEG analysis with three batches, can I use 1 group in all three batches to correct for the batch effect?
Entering edit mode
Last seen 5 weeks ago
United States

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?

DESeq2 • 939 views
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Last seen 21 hours ago
United States

You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.


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