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log2fc
•
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1
vote
10
replies
5.9k
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DESEQ2: apparently wrong log2(fold-change) calculation
deseq2
differential gene expression
log2fc
8.1 years ago
Osvaldo
▴ 40
0
votes
2
replies
634
views
Why my log2fcs are too high?
DESeq2
SingleCell
log2FC
12 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 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
Vani
▴ 20
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
1
vote
5
replies
2.4k
views
log2FC calculation in EdgeR
edger
log2FC
written 4.5 years ago by
matteo.buti
• 0
1
vote
4
replies
1.3k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
16 months ago
Iwan
• 0
2
votes
4
replies
1.4k
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
686
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2
LRT
multifactorial
up/down-reg
log2FC
updated 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Laia
▴ 10
0
votes
4
replies
4.3k
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
42k • 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
42k • 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
42k • written 7.5 years ago by
David R
▴ 90
1
vote
3
replies
5.2k
views
log2 fold change calculation for DE gene analysis
deseq2
L2FC
log2fc
updated 6.8 years ago by
Michael Love
42k • written 6.8 years ago by
sup230
▴ 30
15 results • Page
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Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go! And for comparisons between the cohorts I presume duplicateCorrelation with standar…
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Votes
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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