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logFC
•
reset
16
votes
14
replies
36k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 17 months ago by
OE
• 0 • written 6.4 years ago by
cms72
▴ 20
5
votes
4
replies
20k
views
Report and compare log2FC vs FC
deseq2
logfc
updated 8.7 years ago by
smoorthie
▴ 10 • written 8.7 years ago by
Catalina Aguilar Hurtado
▴ 80
7
votes
6
replies
18k
views
Conversion of LogFC to FC
limma
logfc
fc
updated 3.8 years ago by
Gordon Smyth
49k • written 3.8 years ago by
nia
▴ 30
1
vote
5
replies
11k
views
Limma LogFC hand calculation
limma
logfc
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
cookm346
• 0
1
vote
6
replies
6.0k
views
fold change calculation in edger
edger
normalization
logfc
updated 7.9 years ago by
Michael Love
41k • written 7.9 years ago by
tonja.r
▴ 80
6
votes
2
replies
5.3k
views
What is logFC and "B" in methylation analysis ??
limma
champ
logfc
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
AST
▴ 60
2
votes
1
reply
3.7k
views
Difference between DESeq2 versions and explanation of betaPrior = False and padj
DESeq2
LogFC
Adjusted pvalue
updated 8.9 years ago by
Michael Love
41k • written 8.9 years ago by
madal
• 0
1
vote
8
replies
3.5k
views
Intepretation of RUVseq/edgeR logFC
RUVseq
logFC
edgeR
8.6 years ago
Marie
• 0
0
votes
3
replies
3.4k
views
[limma - v. 17 June 2014] Log2 or not to log2 the data? (Agilent single-channel microarray data)
limma
logFC
normalizeBetweenArrays()
9.1 years ago
FAVI
• 0
4
votes
4
replies
3.1k
views
Determining direction of logFC in limma
logFC
limma
8.1 years ago
pt2395
• 0
1
vote
3
replies
2.8k
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 10 months ago by
Gordon Smyth
49k • written 5.2 years ago by
ZihaoXing
• 0
5
votes
5
replies
2.7k
views
Why the log fold change of some genes returned by edgeR is not compatible with their related FPKM value?
edgeR
logFC
FPKM
updated 7.2 years ago by
Gordon Smyth
49k • written 7.2 years ago by
Sara
▴ 10
0
votes
6
replies
2.4k
views
paired analysis using metagenomeSeq
metagenomeseq
logfc
paired samples
standard error
updated 16 months ago by
tom830979
• 0 • written 7.2 years ago by
manasishah86
▴ 30
3
votes
4
replies
2.3k
views
Calculation of logFC in edgeR
edgeR
logfc
updated 2.9 years ago by
Kevin Blighe
3.9k • written 2.9 years ago by
H
▴ 20
2
votes
2
replies
2.2k
views
limma: Using log2 fold changes as input for a linear model fit
limma
logfc
lmfit
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
Moritz E. Beber
▴ 10
2
votes
4
replies
2.1k
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 5.3 years ago by
Biomed
• 0
1
vote
5
replies
2.0k
views
Why the p value and logFC calculated by limma is so small
limma
volcanoplot
pvalue
logFC
updated 4.8 years ago by
Gordon Smyth
49k • written 4.8 years ago by
xingxd16
▴ 20
4
votes
9
replies
2.0k
views
LIMMA gives different logFC
limma
LogFC
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
beginner
• 0
1
vote
3
replies
1.6k
views
confusing output from EdgeR Glm
edger
logfc
pvalue
updated 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
amoltej
▴ 10
1
vote
1
reply
1.6k
views
Data handling in DESeq2
deseq2
data handling
comparing more than two groups
normalization
logfc
updated 8.1 years ago by
Michael Love
41k • written 8.1 years ago by
bioboy
• 0
9
votes
7
replies
1.6k
views
EdgeR returns small logFC values when using GLM approach
edger
glm
logfc
7.7 years ago
gergely.zsuzsa.n
• 0
4
votes
6
replies
1.5k
views
LogFC values in edgeR - w/wo intercept
design.matrix
logFC
intercept
edgeR
model.matrix
18 months ago
JK Kim
▴ 20
0
votes
1
reply
1.4k
views
Question on fold change calculation for microarray data
logfc
limma
fold change
updated 7.3 years ago by
Gordon Smyth
49k • written 7.3 years ago by
Claudia
▴ 10
1
vote
4
replies
1.2k
views
Methylation EPIC annotation - the logFC values represented as boxplots
probe to gene id
logFC
illuminahumanmethylationepicanno.ilm10b2.hg19
limma contrast matrix
updated 5.7 years ago by
James W. MacDonald
64k • written 5.7 years ago by
jonellevillar
• 0
4
votes
2
replies
1.2k
views
Limma: how to interpret logFC for interaction contrast
limma
logFC
factor interaction
updated 3.5 years ago by
James W. MacDonald
64k • written 3.5 years ago by
Natalia
• 0
2
votes
4
replies
1.0k
views
edgeR output doubts
logFC
edgeR
DifferentialExpression
scRNAseq
2.3 years ago
mbenegas
• 0
0
votes
0
replies
683
views
DEP package - Understanding the results table
dep
proteomics
logFC
4.2 years ago
rina
▴ 30
3
votes
1
reply
594
views
logFC in limma
limma
logFC
updated 3.9 years ago by
James W. MacDonald
64k • written 3.9 years ago by
gv
▴ 40
0
votes
0
replies
255
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue
logFC
lrtest
MAST
7 months ago
Tadeoye
• 0
29 results • Page
1 of 1
Recent ...
Replies
Answer: What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)
by
James W. MacDonald
64k
There are two types of probes used by Illumina. The type I probes bind directly to the CpG site and have two different probes (one for a me…
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
Michael Love
41k
Then for the remaining genes that you don't think are DE, just plot like this: ``` dds_sub <- dds[,dds$condition %in% c("x","y")] dropleve…
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
samer
• 0
yes i turned it off @mikelove
Answer: autonomics: example("read_somascan", package = "autonomics") fails, but not on B
by
Mike Smith
★ 6.2k
It looks like `autonomics` uses `BiocFileCache` to create a local copy of the data and save repeat downloading. Given the (relatively) rec…
Answer: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
Michael Love
41k
I notice you are using `betaPrior=TRUE`. We have set to default and recommended `betaPrior=FALSE` for many years (since version 1.16 in 201…
Votes
Answer: WGCNA documentation not available
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Answer: Correct the batch effect in methylation analysis in R
Comment: Why is DMRcate not available for Bioconductor version 3.18?
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