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significance
•
reset
1
vote
8
replies
2.1k
views
DESeq2: betaPrior changes significance dramatically
deseq2
betaPrior
shrinkage
significance
4.0 years ago
brynedal
▴ 30
1
vote
1
reply
753
views
Beta Value Analysis - DNA Methylation Dataset
dna methylation
illimina 450k methylation
beta
M
significance
updated 4.6 years ago by
James W. MacDonald
59k • written 4.6 years ago by
skids121
• 0
3
votes
3
replies
636
views
limma decideTests: only p-value less than (but not equal to) alpha are flagged as significant
limma
edger
significance
rnaseq
updated 5.2 years ago by
Gordon Smyth
45k • written 5.2 years ago by
roberto.spreafico
▴ 20
1
vote
4
replies
737
views
comparing transcripts expression between conditions
salmon
transcripts
significance
counts
5.8 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
3
replies
1.9k
views
Wald vs LRT: different number of significant genes when testing the same coefficient
deseq2
wald
lrt
genes
significance
updated 5.9 years ago by
Michael Love
36k • written 5.9 years ago by
aziza
▴ 20
0
votes
0
replies
511
views
cell analysis- significance output perturbed in shiny environment
cellcode
significance
6.0 years ago
christopher.clarskon15
▴ 20
6 results • Page
1 of 1
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Replies
Comment: Variance explained (coefficient of determination) in edgeR
by
Gemma
• 0
Many thanks for your answer. To clarify the last point, `R2_nox1` is the proportion of the deviance explained when considering `design.no…
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors
by
Rory Stark
★ 4.4k
The latest version, `DiffBind_3.6.1`, contains fixes for these issues. You will get these fixes if you upgrade to `R_4.2.0` and `Bioconduct…
Comment: Variance explained (coefficient of determination) in edgeR
by
Gordon Smyth
45k
The R2 values look completely normal. The median R2 is 10%, which seems somewhat low rather than high. With so many genes, you will natural…
Comment: Variance explained (coefficient of determination) in edgeR
by
Gemma
• 0
Many thanks, that seems to work! However, the estimates tend to be surprisingly high, for many genes R2 being close to 1 (quartiles being…
Answer: EnrichGO not working with db created from annotationhub
by
Lucía
• 0
I've gone through my code and I'm pretty sure the issue is not the code, but that some gene IDs (all the ones that start with LOC) are just…
Votes
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
Answer: Use MulticoreParam under BatchtoolsParam
Answer: Variance explained (coefficient of determination) in edgeR
HTSeq Counts no longer available
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Johannes Rainer
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Julie Zhu
★ 4.3k
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