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MLSC MANIPAL
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Comment: DESeq2- Mysterious interaction suppresses DEGs
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Thanks so much for your comment. Yes, this makes sense to me, especially since the effect of the drug is subtle. But it raises a larger con…
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Seems OK to me.
```
> dat <- ReadAffy()
> dat
AffyBatch object
size of arrays=744x744 features (20 kb)
cdf=HG-U219 (49386 affyids)
…
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Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make …
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It appears that batch is orthogonal to the treatment, so you can just fit a batch effect in your model.
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