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shrinkage
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DESeq2: betaPrior changes significance dramatically
deseq2
betaPrior
shrinkage
significance
6.0 years ago
brynedal
▴ 40
2
votes
8
replies
2.3k
views
DESeq2 : log2FC discrepencies between results and lfcShrink
deseq2
shrinkage
updated 17 months ago by
Michael Love
42k • written 4.2 years ago by
Nicolas Rosewick
▴ 10
0
votes
3
replies
1.4k
views
disagreement between log2FoldChange and lfcMLE in DESeq2
deseq2
log2fc
shrinkage
updated 6.4 years ago by
Michael Love
42k • written 6.4 years ago by
aec
▴ 90
0
votes
2
replies
1.2k
views
DESeq2: qualitatively different results between deseq2 v1.14 and deseq2 v1.22 when run with shrinkage
deseq2
shrinkage
updated 5.3 years ago by
Michael Love
42k • written 5.3 years ago by
vvi
• 0
0
votes
2
replies
841
views
running apeglm on a normal model and multiple coefficients
shrinkage
apeglm
2.0 years ago
Frederik Ziebell
▴ 20
1
vote
3
replies
572
views
DESeq differential expression results are too stringet. How to relax my criteria
shrinkage
DifferentialExpression
DESeq2
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
Abir.khazaal
▴ 10
6 results • Page
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Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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