In a 3 group DEG analysis with three batches, can I use 1 group in all three batches to correct for the batch effect?
1
0
Entering edit mode
@84c115fa
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
ADD COMMENT
0
Entering edit mode
@mikelove
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.

ADD COMMENT

Login before adding your answer.

Traffic: 680 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6