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logFC
•
reset
17
votes
14
replies
57k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 3.7 years ago by
OE
• 0 • written 8.6 years ago by
cms72
▴ 20
9
votes
7
replies
2.5k
views
EdgeR returns small logFC values when using GLM approach
edger
glm
logfc
9.9 years ago
gergely.zsuzsa.n
• 0
8
votes
2
replies
7.4k
views
What is logFC and "B" in methylation analysis ??
limma
champ
logfc
updated 10.1 years ago by
Aaron Lun
★ 29k • written 10.1 years ago by
AST
▴ 60
7
votes
6
replies
31k
views
Conversion of LogFC to FC
limma
logfc
fc
updated 6.0 years ago by
Gordon Smyth
53k • written 6.0 years ago by
nia
▴ 20
5
votes
5
replies
3.9k
views
Why the log fold change of some genes returned by edgeR is not compatible with their related FPKM value?
edgeR
logFC
FPKM
updated 9.4 years ago by
Gordon Smyth
53k • written 9.4 years ago by
Sara
▴ 20
5
votes
4
replies
25k
views
Report and compare log2FC vs FC
deseq2
logfc
updated 11.0 years ago by
smoorthie
▴ 10 • written 11.0 years ago by
Catalina Aguilar Hurtado
▴ 90
5
votes
6
replies
3.1k
views
LogFC values in edgeR - w/wo intercept
design.matrix
logFC
intercept
edgeR
model.matrix
3.8 years ago
JK Kim
▴ 30
4
votes
4
replies
4.5k
views
Determining direction of logFC in limma
logFC
limma
10.3 years ago
pt2395
• 0
4
votes
9
replies
3.4k
views
LIMMA gives different logFC
limma
LogFC
updated 9.8 years ago by
Aaron Lun
★ 29k • written 9.8 years ago by
beginner
• 0
4
votes
2
replies
2.5k
views
Limma: how to interpret logFC for interaction contrast
limma
logFC
factor interaction
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
Natalia
• 0
3
votes
1
reply
1.1k
views
logFC in limma
limma
logFC
updated 6.2 years ago by
James W. MacDonald
68k • written 6.2 years ago by
gv
▴ 30
3
votes
4
replies
4.5k
views
Calculation of logFC in edgeR
edgeR
logfc
updated 5.1 years ago by
Kevin Blighe
★ 4.0k • written 5.1 years ago by
H
▴ 20
2
votes
4
replies
3.2k
views
Why my limma DEG result in top Table all without significant meaning,showing logFC <1.5 or logFC>-1.5 ?
limma
toptable
deg
logfc
written 7.5 years ago by
Biomed
• 0
2
votes
2
replies
3.0k
views
limma: Using log2 fold changes as input for a linear model fit
limma
logfc
lmfit
updated 10.8 years ago by
Aaron Lun
★ 29k • written 10.8 years ago by
Moritz E. Beber
▴ 10
2
votes
4
replies
2.1k
views
edgeR output doubts
logFC
edgeR
DifferentialExpression
scRNAseq
4.6 years ago
mbenegas
▴ 10
2
votes
1
reply
4.5k
views
Difference between DESeq2 versions and explanation of betaPrior = False and padj
DESeq2
LogFC
Adjusted pvalue
updated 11.2 years ago by
Michael Love
43k • written 11.2 years ago by
madal
• 0
1
vote
1
reply
2.2k
views
Data handling in DESeq2
deseq2
data handling
comparing more than two groups
normalization
logfc
updated 10.3 years ago by
Michael Love
43k • written 10.3 years ago by
bioboy
• 0
1
vote
8
replies
4.5k
views
Intepretation of RUVseq/edgeR logFC
RUVseq
logFC
edgeR
10.9 years ago • updated 10.8 years ago
Marie
• 0
1
vote
3
replies
2.3k
views
confusing output from EdgeR Glm
edger
logfc
pvalue
updated 10.5 years ago by
Aaron Lun
★ 29k • written 10.5 years ago by
amoltej
▴ 10
1
vote
6
replies
7.7k
views
fold change calculation in edger
edger
normalization
logfc
updated 10.2 years ago by
Michael Love
43k • written 10.2 years ago by
tonja.r
▴ 80
1
vote
5
replies
16k
views
Limma LogFC hand calculation
limma
logfc
updated 9.8 years ago by
Aaron Lun
★ 29k • written 9.8 years ago by
cookm346
• 0
1
vote
4
replies
2.1k
views
Methylation EPIC annotation - the logFC values represented as boxplots
probe to gene id
logFC
illuminahumanmethylationepicanno.ilm10b2.hg19
limma contrast matrix
updated 7.9 years ago by
James W. MacDonald
68k • written 7.9 years ago by
jonellevillar
• 0
1
vote
3
replies
5.2k
views
the results of logFC is base e (log(FC,base=exp(1)) or base 2 (log2FC) ,is logFC same as log2FC in edgeR?
edger
limma
logfc
updated 3.1 years ago by
Gordon Smyth
53k • written 7.5 years ago by
ZihaoXing
• 0
1
vote
5
replies
4.1k
views
Why the p value and logFC calculated by limma is so small
limma
volcanoplot
pvalue
logFC
updated 7.0 years ago by
Gordon Smyth
53k • written 7.0 years ago by
xingxd16
▴ 20
0
votes
0
replies
1.3k
views
DEP package - Understanding the results table
dep
proteomics
logFC
6.4 years ago
rina
▴ 30
0
votes
6
replies
3.4k
views
paired analysis using metagenomeSeq
metagenomeseq
logfc
paired samples
standard error
updated 3.6 years ago by
tom830979
• 0 • written 9.5 years ago by
manasishah86
▴ 30
0
votes
0
replies
1.1k
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue
logFC
lrtest
MAST
2.9 years ago
Tadeoye
▴ 20
0
votes
1
reply
2.0k
views
Question on fold change calculation for microarray data
logfc
limma
fold change
updated 9.5 years ago by
Gordon Smyth
53k • written 9.5 years ago by
Claudia
▴ 10
0
votes
3
replies
4.4k
views
[limma - v. 17 June 2014] Log2 or not to log2 the data? (Agilent single-channel microarray data)
limma
logFC
normalizeBetweenArrays()
11.3 years ago
FAVI
• 0
29 results • Page
1 of 1
Recent ...
Replies
Answer: Quick two questions on limpa
by
Gordon Smyth
53k
Thanks for your questions about limpa. The short answer is that you should use the default settings of the readSpectronaut() function. The…
Comment: ComplexHeatmap removes row labels if annotation is added
by
RosaliaSchulist99
• 0
thanks for sharing https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#automatic-adjustment-to-the-main-heatmap
Comment: ComplexHeatmap removes row labels if annotation is added
by
RosaliaSchulist99
• 0
thanks for sharing
Comment: recursively counting package dependencies
by
Helena
• 0
Aha, yes, totally forgot the `Depends` field... I tried with both `Imports/Depends/LinkingTo` and without `LinkingTo` ... I think this is r…
Answer: recursively counting package dependencies
by
ATpoint
★ 5.0k
Based on https://stat.ethz.ch/pipermail/bioc-devel/2021-October/018596.html it is something like ```r db <- available.packages(repos = …
Votes
Comment: tximeta cannot open annotation gtf?
Answer: tximeta cannot open annotation gtf?
Comment: Question about using LRT test for time course experiments with DESeq2
A: DESeq2 LRT test for multi-factor designs
Answer: RNA Seq using Lrt
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