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betaPrior
•
reset
1
vote
8
replies
3.8k
views
DESeq2: betaPrior changes significance dramatically
deseq2
betaPrior
shrinkage
significance
6.0 years ago
brynedal
▴ 40
5
votes
4
replies
2.1k
views
lfcShrink behavior with homogeneous expression dataset
deseq2
lfcshrink
betaprior
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
mat.lesche
▴ 90
0
votes
6
replies
1.5k
views
large range of LFC in DESeq2
deseq2
lfc
betaprior
updated 18 months ago by
Michael Love
41k • written 5.4 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 7.7 years ago by
thomas.siegmund
• 0 • written 7.7 years ago by
akaever
▴ 30
2
votes
1
reply
1.3k
views
LRT test with or without betaPrior
deseq2
LRT
betaprior
updated 7.6 years ago by
Michael Love
41k • written 7.6 years ago by
laianavarromartin
▴ 20
1
vote
3
replies
1.1k
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 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
tarun2
• 0
6 results • Page
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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