Batch correction for two conditions two batches
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KRA • 0
@kra-12378
Last seen 4.7 years ago

Hello,

If I have two conditions, which were sequenced as two different runs, is there a way to normalize the data before running DESeq2?

For example: I have 8 samples 4 each of one condition age1, batch1 age1, batch1 age1, batch1 age1, batch1 age2, batch2 age2, batch2 age2, batch2 age2, batch2 Is there a way to normalize the impact of batch on these samples, before I do a differential expression analysis?

deseq2 • 646 views
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swbarnes2 ★ 1.3k
@swbarnes2-14086
Last seen 16 hours ago
San Diego

There is no way to separate the effect of batch from condition when they are completely confounded.

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Thanks swbarnes !! I was thinking the same but wanted to confirm before I conclude on it.

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