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Comment: Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Ana
by
Michael Love
43k
And to add to this: when you put a generic package (e.g. DESeq2) as a tag, it actually emails the maintainer.
Answer: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
TPM is fine, I've also sometimes used TPM with some robust column scaling, e.g.:
```
sf <- DESeq2::estimateSizeFactorsForMatrix(txi$abu…
Comment: Using TPM from tximport of Salmon output for singscore
by
ATpoint
★
4.7k
As a comment, TMM does not apply here because the authors say in the article that they recommend gene length bias to be removed, and TMM do…
Comment: Surprising behavior for DEXseq dispersion estimate plot?
by
Esperan
•
0
The absence of correlation with feature lengths and other parameters like adjusted p-values and log fold change values can indicate that th…
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
by
Gordon Smyth
52k
> Specific Question 1: Is there a preferred paradigm for voomLmFit for paired RNA-seq between blocking on individual and including individu…
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