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Comment: Mostly increased counts in differentially accessible peaks using DESeq2
by
ATpoint
★
4.5k
Keep in mind that if you add replication then you should do it for all conditions so you can meaningfully regress the inevitable batch effe…
Answer: Automatically generate contrasts from a model matrix / formula
by
Gordon Smyth
51k
I am very concerned that you are attempting to extract pairwise comparisons from an interaction formula like `0 + Group*Sex + Age`, because…
Comment: Mostly increased counts in differentially accessible peaks using DESeq2
by
Ricardo Iván
•
0
Hi Michael,
Thanks for your reply. After reviewing the PCAs, maybe the issue that despite the replicates looking similar, there is still a…
Comment: Using Normalized Counts in DESeq2
by
Michael Love
42k
Also, just to add, there are many dozens of posts on this topic of DESeq2 applied to TCGA counts, normalized or other. Recommend google sea…
Answer: Using Normalized Counts in DESeq2
by
ATpoint
★
4.5k
TCGA raw counts can be obtained for example using the TCGAbiolinks or recount packages.
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