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Comment: Input Question for deseq.r
by
ATpoint
★
4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present
by
ATpoint
★
4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded
by
ATpoint
★
4.0k
```r
> table(batch, group)
group
batch egfr gfp her2
1 0 12 5
2 6 6 0
```
All of her2 is batch2, all of egfr i…
Comment: DESeq2 setting significant p-value
by
Dev
•
0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format
I have …
Comment: DESeq filtering specific to contrasts
by
Carlin95
•
0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
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