Showing : significance • reset
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DESeq2: betaPrior changes significance dramatically
deseq2 betaPrior shrinkage significance
4.0 years ago brynedal ▴ 30
1
vote
1
reply
753
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Beta Value Analysis - DNA Methylation Dataset
dna methylation illimina 450k methylation beta M significance
updated 4.6 years ago by 59k • written 4.6 years ago by • 0
3
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3
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636
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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 45k • written 5.2 years ago by ▴ 20
1
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4
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737
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comparing transcripts expression between conditions
salmon transcripts significance counts
5.8 years ago Assa Yeroslaviz ★ 1.5k
0
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3
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1.9k
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Wald vs LRT: different number of significant genes when testing the same coefficient
deseq2 wald lrt genes significance
updated 5.9 years ago by 36k • written 5.9 years ago by ▴ 20
0
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0
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511
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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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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
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