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Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
•
0
Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0
![enter image description here][1]…
Answer: DESeq2 - am I extracting results incorrectly?
by
James W. MacDonald
68k
If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
•
0
I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…
Answer: Origin of the labels for the SingleCellMultiModal dataset
by
ATpoint
★
4.8k
If you check the underlying code a bit you find that there is a file with data sources:
```r
modes_file <- system.file("extdata", "metadat…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
ATpoint
★
4.8k
That plot looks extremely worrying. You have very unbalanced DE profiles and clearly two populations of peaks on the right. I would make su…
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