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betaprior
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8
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DESeq2: betaPrior changes significance dramatically
deseq2
betaPrior
shrinkage
significance
5.9 years ago
brynedal
▴ 40
5
votes
4
replies
2.0k
views
lfcShrink behavior with homogeneous expression dataset
deseq2
lfcshrink
betaprior
updated 5.7 years ago by
Michael Love
41k • written 5.7 years ago by
mat.lesche
▴ 90
0
votes
6
replies
1.4k
views
large range of LFC in DESeq2
deseq2
lfc
betaprior
updated 17 months ago by
Michael Love
41k • written 5.3 years ago by
Mariaxi
• 0
0
votes
7
replies
1.3k
views
Highly differentially expressed genes not found with DESeq2 and default betaPrior
deseq2
betaprior
updated 7.6 years ago by
thomas.siegmund
• 0 • written 7.6 years ago by
akaever
▴ 30
2
votes
1
reply
1.2k
views
LRT test with or without betaPrior
deseq2
LRT
betaprior
updated 7.5 years ago by
Michael Love
41k • written 7.5 years ago by
laianavarromartin
▴ 20
1
vote
3
replies
1.0k
views
DESEq2: the use of interaction term and grouping with different betaPrior arguments in older version of DESEq2
deseq2
interaction term
multiple groups
betaprior
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
tarun2
• 0
6 results • Page
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Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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