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Log2FC
•
reset
0
votes
2
replies
663
views
Why my log2fcs are too high?
DESeq2
SingleCell
log2FC
13 months ago
paria.alipour
• 0
1
vote
4
replies
1.4k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
17 months ago
Iwan
• 0
0
votes
1
reply
709
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2
LRT
multifactorial
up/down-reg
log2FC
updated 18 months ago by
James W. MacDonald
66k • written 18 months ago by
Laia
▴ 10
0
votes
4
replies
4.5k
views
Understanding the Log2FoldChange calculated with DESeq2 and according to formula log2(treated/control)
DESeq2
log2FC
21 months ago
User000
• 0
2
votes
4
replies
1.4k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 23 months ago by
Gordon Smyth
51k • written 23 months ago by
Yang Shi
▴ 10
1
vote
5
replies
2.4k
views
log2FC calculation in EdgeR
edger
log2FC
written 4.6 years ago by
matteo.buti
• 0
2
votes
4
replies
1.3k
views
Standard error of log2FC from DESeq in time series experiment
deseq2
log2fc
standard error
timecourse
updated 6.3 years ago by
ellascottgm
• 0 • written 6.4 years ago by
Verena
• 0
0
votes
3
replies
1.4k
views
disagreement between log2FoldChange and lfcMLE in DESeq2
deseq2
log2fc
shrinkage
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
aec
▴ 90
1
vote
3
replies
5.3k
views
log2 fold change calculation for DE gene analysis
deseq2
L2FC
log2fc
updated 6.9 years ago by
Michael Love
42k • written 6.9 years ago by
sup230
▴ 30
0
votes
2
replies
3.9k
views
DESEq2 log2FoldChange and lfcSE calculations
deseq2
log2fc
updated 7.6 years ago by
Michael Love
42k • written 7.6 years ago by
David R
▴ 90
2
votes
2
replies
2.0k
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 8.0 years ago by
Michael Love
42k • written 8.0 years ago by
robin.uchiyama
• 0
6
votes
8
replies
5.9k
views
Does limma calculate pvalues using log2 fold changes or with linear values?
limma
pvalue
log2fc
log2
updated 18 months ago by
James W. MacDonald
66k • written 8.2 years ago by
serpalma.v
▴ 60
1
vote
10
replies
5.9k
views
DESEQ2: apparently wrong log2(fold-change) calculation
deseq2
differential gene expression
log2fc
8.2 years ago
Osvaldo
▴ 40
1
vote
3
replies
2.3k
views
Log2 foldchange in DESeq2
deseq2
R
log2fc
updated 8.5 years ago by
Michael Love
42k • written 8.5 years ago by
Sushant Pawar
• 0
1
vote
5
replies
1.8k
views
Log2FC values very small with SCAN
scan
Log2FC
updated 8.9 years ago by
Gordon Smyth
51k • written 8.9 years ago by
Vani
▴ 20
15 results • Page
1 of 1
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Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
Michael Love
42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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