updated 9 weeks ago by
Gordon Smyth
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written 9 weeks ago by
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Answer: Using Normalized Counts in DESeq2
by
ATpoint
★
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
by
Christine Jones
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Fantastic, thank you
Comment: When running contrasts, does it use normalized read counts?
by
Katherine
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0
Ok, so the comment I was given where they said DeSeq2 should be with normalized counts is incorrect.
the ```normalized_counts``` variable …
Answer: How to reverse complement some elements of a DNAStringSet
by
James W. MacDonald
67k
You should always try the vectorized method first, rather than looping.
```
> myFasta[myFasta_rc] <- reverseComplement(myFasta[myFasta_…
Answer: When running contrasts, does it use normalized read counts?
by
James W. MacDonald
67k
A contrast is a comparison of two or more coefficients. When you run `nbiomWaldTest` you are fitting the GLM and estimating coefficients. T…
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