updated 20 months ago by
thomas.nigel.lawson
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written 24 months ago by
hp71727
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Comment: Mostly increased counts in differentially accessible peaks using DESeq2
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Ricardo Iván
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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
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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
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4.5k
TCGA raw counts can be obtained for example using the TCGAbiolinks or recount packages.
Comment: How to reverse complement some elements of a DNAStringSet
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Christine Jones
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Fantastic, thank you
Comment: When running contrasts, does it use normalized read counts?
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Katherine
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Ok, so the comment I was given where they said DeSeq2 should be with normalized counts is incorrect.
the ```normalized_counts``` variable …
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