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One-sided p-value from DESeq2
DESeq2 nbinomWaldTest one-sided p-value
updated 6.1 years ago by 42k • written 6.1 years ago by ▴ 170
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What does one-sided p-value in DESeq2 mean in biological terms?
one-sided nbinomWaldTest p-value meta-analysis DESeq2
updated 3.1 years ago by 42k • written 3.1 years ago by • 0
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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.
Comment: How to reverse complement some elements of a DNAStringSet by Christine Jones • 0
Fantastic, thank you
Comment: When running contrasts, does it use normalized read counts? by Katherine • 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_…
Votes
Answer: When running contrasts, does it use normalized read counts?
Comment: featureCounts fails to load annotation file
Answer: How to reverse complement some elements of a DNAStringSet
Answer: KEGGgraph result difference
Answer: What should be the normalization protocol for RNA seq data for WGCNA?
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