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Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge
beta
DESeq2
9 months ago
Ndimensional
▴ 20
2
votes
6
replies
1.0k
views
Limma beta coefficient confidence intervals
limma
limmaGUI
beta
21 months ago
fluentin44
• 0
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1.4k
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Beta Value Analysis - DNA Methylation Dataset
dna methylation
illimina 450k methylation
beta
M
significance
updated 6.5 years ago by
James W. MacDonald
65k • written 6.5 years ago by
skids121
• 0
3 results • Page
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Comment: error when using M-values in ChAMP
by
hortenseguillaume96
• 0
Hello Tian, I'd like to get the M-values matrix so that I can carry out a linear regression study. However, when I apply the champ.load fu…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
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