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Comment: stat value is throwed out after lfcShrink in DESeq2
by
AngelaAmari
• 0
Sometimes there is still quite a few ties even for shrunken LFC. Can we use the so called posterior t-stat for breaking the ties, or LFC * …
Comment: Questions in Regards to LFC shrinkage in DESeq2
by
Gordon
• 0
I read the paper previously as well as: https://introtogenomics.readthedocs.io/en/latest/2021.11.11.DeseqTutorial.html To clarify, is the …
Answer: Questions in Regards to LFC shrinkage in DSeq2
by
ATpoint
★ 4.3k
The correct (that is recommended by the developer) way is summarized in the vignette, please have a look, or state more precisely what the …
Answer: Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multip
by
gabriel.hoffman
▴ 150
1. You should always use `voomWithDreamWeights()` on the counts before fitting the model. This produces log2 CPM and computes precision …
Comment: Gene filtering in DESeq2
by
ATpoint
★ 4.3k
Either this, or use `filterByExpr` from edgeR. Not that this is necessarily better, but it is heavily used and stood well the test of time.…
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Questions in Regards to LFC shrinkage in DESeq2
Answer: Gene filtering in DESeq2
Answer: after calcNormFactors with EdgeR, how to get TMM normalized matrix?
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
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