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log2fc
•
reset
1
vote
13
replies
989
views
Ranking the GSEA Results
fgsea
log2FC
3 months ago • updated 10 weeks ago
V_Vibes
• 0
1
vote
1
reply
279
views
DESeq2 - vst() - log2FC - no replicates
DESeq2
log2FC
vst()
updated 3 months ago by
ATpoint
★ 4.4k • written 3 months ago by
lifeonmars
• 0
0
votes
2
replies
779
views
Why my log2fcs are too high?
DESeq2
SingleCell
log2FC
17 months ago
paria.alipour
• 0
1
vote
4
replies
1.7k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
21 months ago
Iwan
• 0
0
votes
1
reply
861
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2
LRT
multifactorial
up/down-reg
log2FC
updated 21 months ago by
James W. MacDonald
67k • written 21 months ago by
Laia
▴ 10
0
votes
4
replies
5.1k
views
Understanding the Log2FoldChange calculated with DESeq2 and according to formula log2(treated/control)
DESeq2
log2FC
2.0 years ago
User000
• 0
2
votes
4
replies
1.6k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 2.2 years ago by
Gordon Smyth
51k • written 2.2 years ago by
Yang Shi
▴ 10
1
vote
5
replies
2.7k
views
log2FC calculation in EdgeR
edger
log2FC
written 4.9 years ago by
matteo.buti
• 0
2
votes
4
replies
1.5k
views
Standard error of log2FC from DESeq in time series experiment
deseq2
log2fc
standard error
timecourse
updated 6.6 years ago by
ellascottgm
• 0 • written 6.6 years ago by
Verena
• 0
0
votes
3
replies
1.5k
views
disagreement between log2FoldChange and lfcMLE in DESeq2
deseq2
log2fc
shrinkage
updated 6.8 years ago by
Michael Love
42k • written 6.8 years ago by
aec
▴ 90
1
vote
3
replies
5.7k
views
log2 fold change calculation for DE gene analysis
deseq2
L2FC
log2fc
updated 7.1 years ago by
Michael Love
42k • written 7.1 years ago by
sup230
▴ 30
0
votes
2
replies
4.1k
views
DESEq2 log2FoldChange and lfcSE calculations
deseq2
log2fc
updated 7.9 years ago by
Michael Love
42k • written 7.9 years ago by
David R
▴ 90
2
votes
2
replies
2.1k
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 8.3 years ago by
Michael Love
42k • written 8.3 years ago by
robin.uchiyama
• 0
6
votes
8
replies
6.2k
views
Does limma calculate pvalues using log2 fold changes or with linear values?
limma
pvalue
log2fc
log2
updated 22 months ago by
James W. MacDonald
67k • written 8.5 years ago by
serpalma.v
▴ 60
1
vote
10
replies
6.1k
views
DESEQ2: apparently wrong log2(fold-change) calculation
deseq2
differential gene expression
log2fc
8.5 years ago
Osvaldo
▴ 40
1
vote
3
replies
2.4k
views
Log2 foldchange in DESeq2
deseq2
R
log2fc
updated 8.8 years ago by
Michael Love
42k • written 8.8 years ago by
Sushant Pawar
• 0
1
vote
5
replies
2.0k
views
Log2FC values very small with SCAN
scan
Log2FC
updated 9.2 years ago by
Gordon Smyth
51k • written 9.2 years ago by
Vani
▴ 20
17 results • Page
1 of 1
Recent ...
Replies
Answer: Poor dispersion fit in DESeq2
by
Michael Love
42k
The fit (red line) doesn't matter because you have so many samples. Note there is almost no shrinkage. Besides that you may be intereste…
Answer: DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days p
by
Michael Love
42k
I'd recommend actually meeting with a local statistician to work out the analysis plan, or someone familiar with linear models in R. I h…
Answer: DESeq2 design and contrasts with 2 drug-treated and one control group
by
Michael Love
42k
> Now I am interested in comparing the DE genes between the resistant and acute groups, but I am unsure how to account for DMSO in that com…
Answer: Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentificat
by
Laurent Gatto
1.6k
Tthis happens because the sequence spectraVariable is expected to be an atomic vector or a List with elements of length 1, but it's not - s…
Comment: How should I run ssGSEA Hallmark Enrichment Analysis?
by
Ginny
• 0
I think the other side of this question is that the non protein coding genes would be in the "background", they would influence the ranking…
Votes
Answer: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: addPatternDensity in 'qsea' takes too much time
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