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log2fc
•
reset
1
vote
13
replies
1.9k
views
Ranking the GSEA Results
fgsea
log2FC
10 months ago
V_Vibes
• 0
1
vote
1
reply
612
views
DESeq2 - vst() - log2FC - no replicates
DESeq2
log2FC
vst()
updated 11 months ago by
ATpoint
★ 4.8k • written 11 months ago by
lifeonmars
• 0
0
votes
2
replies
1.0k
views
Why my log2fcs are too high?
DESeq2
SingleCell
log2FC
2.1 years ago
paria.alipour
• 0
1
vote
4
replies
2.3k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
2.4 years ago
Iwan
• 0
0
votes
1
reply
1.0k
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2
LRT
multifactorial
up/down-reg
log2FC
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
Laia
▴ 10
0
votes
4
replies
6.4k
views
Understanding the Log2FoldChange calculated with DESeq2 and according to formula log2(treated/control)
DESeq2
log2FC
2.7 years ago
User000
• 0
2
votes
4
replies
1.8k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 2.8 years ago by
Gordon Smyth
52k • written 2.8 years ago by
Yang Shi
▴ 10
1
vote
5
replies
3.5k
views
log2FC calculation in EdgeR
edger
log2FC
written 5.6 years ago by
matteo.buti
• 0
2
votes
4
replies
1.7k
views
Standard error of log2FC from DESeq in time series experiment
deseq2
log2fc
standard error
timecourse
updated 7.3 years ago by
ellascottgm
• 0 • written 7.3 years ago by
Verena
• 0
0
votes
3
replies
1.6k
views
disagreement between log2FoldChange and lfcMLE in DESeq2
deseq2
log2fc
shrinkage
updated 7.4 years ago by
Michael Love
43k • written 7.4 years ago by
aec
▴ 90
1
vote
3
replies
6.7k
views
log2 fold change calculation for DE gene analysis
deseq2
L2FC
log2fc
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
sup230
▴ 30
0
votes
2
replies
4.3k
views
DESEq2 log2FoldChange and lfcSE calculations
deseq2
log2fc
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
David R
▴ 90
2
votes
2
replies
2.5k
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 9.0 years ago by
Michael Love
43k • written 9.0 years ago by
robin.uchiyama
• 0
6
votes
8
replies
7.2k
views
Does limma calculate pvalues using log2 fold changes or with linear values?
limma
pvalue
log2fc
log2
updated 2.5 years ago by
James W. MacDonald
68k • written 9.1 years ago by
serpalma.v
▴ 60
1
vote
10
replies
6.4k
views
DESEQ2: apparently wrong log2(fold-change) calculation
deseq2
differential gene expression
log2fc
9.2 years ago
Osvaldo
▴ 40
1
vote
3
replies
2.6k
views
Log2 foldchange in DESeq2
deseq2
R
log2fc
updated 9.5 years ago by
Michael Love
43k • written 9.5 years ago by
Sushant Pawar
• 0
1
vote
5
replies
2.3k
views
Log2FC values very small with SCAN
scan
Log2FC
updated 9.8 years ago by
Gordon Smyth
52k • written 9.8 years ago by
Vani
▴ 20
17 results • Page
1 of 1
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Replies
Answer: Typo in the help of lmFit()
by
Gordon Smyth
52k
Thanks for the heads-up. > The _Details_ in the documentation of lmFit() still says that the default correlation is 0.75 Yes, you're righ…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
by
caroline.zanchi
▴ 10
Thank you ! ![enter image description here][1] In the end I did ```r rn2 <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "GENENAME"…
Answer: Memory issue while using "quickcluster" and "computeSumFactors" functions on sin
by
James W. MacDonald
68k
The obvious solution is to use cloud computing, which is likely cheaper than getting more RAM for your computer.
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
by
James W. MacDonald
68k
``` library(org.Dm.eg.db) rn <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "SYMBOL","FLYBASE") ## ensure no NA values get propaga…
Comment: Discrepancies in normalised count data vs unnormalised
by
AMgroup
• 0
Thank you for your explanation, that makes sense. Do you have any suggestions on how to deal with this issue? if it is an issue? especially…
Votes
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
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