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Log2FC
•
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1
vote
10
replies
5.8k
views
DESEQ2: apparently wrong log2(fold-change) calculation
deseq2
differential gene expression
log2fc
8.1 years ago
Osvaldo
▴ 40
0
votes
2
replies
604
views
Why my log2fcs are too high?
DESeq2
SingleCell
log2FC
11 months ago
paria.alipour
• 0
6
votes
8
replies
5.7k
views
Does limma calculate pvalues using log2 fold changes or with linear values?
limma
pvalue
log2fc
log2
updated 17 months ago by
James W. MacDonald
65k • written 8.1 years ago by
serpalma.v
▴ 60
2
votes
4
replies
1.3k
views
Standard error of log2FC from DESeq in time series experiment
deseq2
log2fc
standard error
timecourse
updated 6.2 years ago by
ellascottgm
• 0 • written 6.2 years ago by
Verena
• 0
1
vote
5
replies
1.8k
views
Log2FC values very small with SCAN
scan
Log2FC
updated 8.7 years ago by
Gordon Smyth
50k • written 8.8 years ago by
Vani
▴ 20
0
votes
3
replies
1.3k
views
disagreement between log2FoldChange and lfcMLE in DESeq2
deseq2
log2fc
shrinkage
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
aec
▴ 90
1
vote
5
replies
2.3k
views
log2FC calculation in EdgeR
edger
log2FC
written 4.5 years ago by
matteo.buti
• 0
1
vote
4
replies
1.2k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
15 months ago
Iwan
• 0
2
votes
4
replies
1.3k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
Yang Shi
▴ 10
0
votes
1
reply
668
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2
LRT
multifactorial
up/down-reg
log2FC
updated 16 months ago by
James W. MacDonald
65k • written 16 months ago by
Laia
▴ 10
0
votes
4
replies
4.1k
views
Understanding the Log2FoldChange calculated with DESeq2 and according to formula log2(treated/control)
DESeq2
log2FC
19 months ago
User000
• 0
1
vote
3
replies
2.3k
views
Log2 foldchange in DESeq2
deseq2
R
log2fc
updated 8.4 years ago by
Michael Love
41k • written 8.4 years ago by
Sushant Pawar
• 0
2
votes
2
replies
1.9k
views
Can I calculate counts from the base mean and log2fc outputs of DESeq2? Also, can I calculate error for counts values from lfcse output?
deseq2
chipseq
counts
log2fc
error
updated 7.9 years ago by
Michael Love
41k • written 7.9 years ago by
robin.uchiyama
• 0
0
votes
2
replies
3.8k
views
DESEq2 log2FoldChange and lfcSE calculations
deseq2
log2fc
updated 7.5 years ago by
Michael Love
41k • written 7.5 years ago by
David R
▴ 90
1
vote
3
replies
5.1k
views
log2 fold change calculation for DE gene analysis
deseq2
L2FC
log2fc
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
sup230
▴ 30
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Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
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Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
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by
prity6459
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Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
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50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
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50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
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