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James W. MacDonald
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Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
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0
Got you. Thanks again for your comments.
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
•
0
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…
Answer: ERROR; return code from pthread_create() is 22
by
James W. MacDonald
65k
Seems OK to me.
```
> dat <- ReadAffy()
> dat
AffyBatch object
size of arrays=744x744 features (20 kb)
cdf=HG-U219 (49386 affyids)
…
Answer: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
65k
Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make …
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
by
James W. MacDonald
65k
It appears that batch is orthogonal to the treatment, so you can just fit a batch effect in your model.
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