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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
2.2k
views
DESeq2 : log2FC discrepencies between results and lfcShrink
deseq2
shrinkage
updated 17 months ago by
Michael Love
41k • written 4.2 years ago by
Nicolas Rosewick
▴ 10
0
votes
3
replies
1.3k
views
disagreement between log2FoldChange and lfcMLE in DESeq2
deseq2
log2fc
shrinkage
updated 6.4 years ago by
Michael Love
41k • 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
41k • written 5.3 years ago by
vvi
• 0
0
votes
2
replies
829
views
running apeglm on a normal model and multiple coefficients
shrinkage
apeglm
2.0 years ago • updated 24 months ago
Frederik Ziebell
▴ 20
1
vote
3
replies
549
views
DESeq differential expression results are too stringet. How to relax my criteria
shrinkage
DifferentialExpression
DESeq2
updated 9 months ago by
ATpoint
★ 4.0k • written 9 months ago by
Abir.khazaal
▴ 10
6 results • Page
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Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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