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log2FC
•
reset
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
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
1
vote
3
replies
5.2k
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
0
votes
4
replies
4.2k
views
Understanding the Log2FoldChange calculated with DESeq2 and according to formula log2(treated/control)
DESeq2
log2FC
19 months ago
User000
• 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
5
replies
2.3k
views
log2FC calculation in EdgeR
edger
log2FC
written 4.5 years ago by
matteo.buti
• 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
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
1.3k
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
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
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
4
replies
1.3k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
15 months ago
Iwan
• 0
0
votes
1
reply
672
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
2
replies
615
views
Why my log2fcs are too high?
DESeq2
SingleCell
log2FC
12 months ago
paria.alipour
• 0
15 results • Page
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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