Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
logFC
•
reset
17
votes
14
replies
46k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 2.5 years ago by
OE
• 0 • written 7.4 years ago by
cms72
▴ 20
7
votes
6
replies
25k
views
Conversion of LogFC to FC
limma
logfc
fc
updated 4.8 years ago by
Gordon Smyth
52k • written 4.8 years ago by
nia
▴ 30
5
votes
4
replies
23k
views
Report and compare log2FC vs FC
deseq2
logfc
updated 9.7 years ago by
smoorthie
▴ 10 • written 9.7 years ago by
Catalina Aguilar Hurtado
▴ 90
1
vote
5
replies
14k
views
Limma LogFC hand calculation
limma
logfc
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 years ago by
cookm346
• 0
1
vote
6
replies
6.7k
views
fold change calculation in edger
edger
normalization
logfc
updated 8.9 years ago by
Michael Love
43k • written 8.9 years ago by
tonja.r
▴ 80
7
votes
2
replies
6.3k
views
What is logFC and "B" in methylation analysis ??
limma
champ
logfc
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
AST
▴ 60
2
votes
1
reply
4.0k
views
Difference between DESeq2 versions and explanation of betaPrior = False and padj
DESeq2
LogFC
Adjusted pvalue
updated 9.9 years ago by
Michael Love
43k • written 9.9 years ago by
madal
• 0
1
vote
8
replies
3.9k
views
Intepretation of RUVseq/edgeR logFC
RUVseq
logFC
edgeR
9.6 years ago
Marie
• 0
0
votes
3
replies
3.9k
views
[limma - v. 17 June 2014] Log2 or not to log2 the data? (Agilent single-channel microarray data)
limma
logFC
normalizeBetweenArrays()
10.1 years ago
FAVI
• 0
1
vote
3
replies
3.8k
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 23 months ago by
Gordon Smyth
52k • written 6.2 years ago by
ZihaoXing
• 0
4
votes
4
replies
3.8k
views
Determining direction of logFC in limma
logFC
limma
9.1 years ago
pt2395
• 0
3
votes
4
replies
3.5k
views
Calculation of logFC in edgeR
edgeR
logfc
updated 3.9 years ago by
Kevin Blighe
★ 4.0k • written 3.9 years ago by
H
▴ 20
5
votes
5
replies
3.3k
views
Why the log fold change of some genes returned by edgeR is not compatible with their related FPKM value?
edgeR
logFC
FPKM
updated 8.2 years ago by
Gordon Smyth
52k • written 8.2 years ago by
Sara
▴ 20
1
vote
5
replies
2.9k
views
Why the p value and logFC calculated by limma is so small
limma
volcanoplot
pvalue
logFC
updated 5.8 years ago by
Gordon Smyth
52k • written 5.8 years ago by
xingxd16
▴ 20
0
votes
6
replies
2.8k
views
paired analysis using metagenomeSeq
metagenomeseq
logfc
paired samples
standard error
updated 2.4 years ago by
tom830979
• 0 • written 8.2 years ago by
manasishah86
▴ 30
4
votes
9
replies
2.7k
views
LIMMA gives different logFC
limma
LogFC
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 years ago by
beginner
• 0
2
votes
4
replies
2.6k
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 6.3 years ago by
Biomed
• 0
2
votes
2
replies
2.6k
views
limma: Using log2 fold changes as input for a linear model fit
limma
logfc
lmfit
updated 9.5 years ago by
Aaron Lun
★ 28k • written 9.5 years ago by
Moritz E. Beber
▴ 10
5
votes
6
replies
2.2k
views
LogFC values in edgeR - w/wo intercept
design.matrix
logFC
intercept
edgeR
model.matrix
2.5 years ago
JK Kim
▴ 20
9
votes
7
replies
2.0k
views
EdgeR returns small logFC values when using GLM approach
edger
glm
logfc
8.7 years ago
gergely.zsuzsa.n
• 0
1
vote
3
replies
2.0k
views
confusing output from EdgeR Glm
edger
logfc
pvalue
updated 9.3 years ago by
Aaron Lun
★ 28k • written 9.3 years ago by
amoltej
▴ 10
1
vote
1
reply
1.9k
views
Data handling in DESeq2
deseq2
data handling
comparing more than two groups
normalization
logfc
updated 9.1 years ago by
Michael Love
43k • written 9.1 years ago by
bioboy
• 0
4
votes
2
replies
1.8k
views
Limma: how to interpret logFC for interaction contrast
limma
logFC
factor interaction
updated 4.5 years ago by
James W. MacDonald
67k • written 4.5 years ago by
Natalia
• 0
0
votes
1
reply
1.7k
views
Question on fold change calculation for microarray data
logfc
limma
fold change
updated 8.3 years ago by
Gordon Smyth
52k • written 8.3 years ago by
Claudia
▴ 10
1
vote
4
replies
1.6k
views
Methylation EPIC annotation - the logFC values represented as boxplots
probe to gene id
logFC
illuminahumanmethylationepicanno.ilm10b2.hg19
limma contrast matrix
updated 6.7 years ago by
James W. MacDonald
67k • written 6.7 years ago by
jonellevillar
• 0
2
votes
4
replies
1.6k
views
edgeR output doubts
logFC
edgeR
DifferentialExpression
scRNAseq
3.3 years ago
mbenegas
▴ 10
0
votes
0
replies
971
views
DEP package - Understanding the results table
dep
proteomics
logFC
5.2 years ago
rina
▴ 30
3
votes
1
reply
846
views
logFC in limma
limma
logFC
updated 4.9 years ago by
James W. MacDonald
67k • written 4.9 years ago by
gv
▴ 40
0
votes
0
replies
700
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue
logFC
lrtest
MAST
20 months ago
Tadeoye
▴ 20
29 results • Page
1 of 1
Recent ...
Replies
Answer: Advice needed: Using limma for differential pathway analysis with continuous dis
by
Gordon Smyth
52k
limma has always handled any combination of continuous or categorical variables from the very beginning. You simply add continuous variable…
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi @yangliao, thanks for the note. We use Feature Counts extensively for gene-level counting (exon features). Unfortunately though, and I…
Comment: Feature Counts - potential bug with outfile.jcounts
by
Yang Liao
▴ 450
When you use `featureCounts` to count junctions with the `-J` option, it doesn't check if the junction is exactly overlap with exons of gen…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
by
ATpoint
★ 4.6k
I think you run into the common pitfall that you treat results as categorical (significant, not significant) whereas in reality the results…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
by
swbarnes2
★ 1.4k
It would probably help if you broke out the raw and normalized read counts for all the samples.
Votes
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: Running multiple KNN queries in parallel
Awards
• All
Popular Question
to
Tadeoye
▴ 20
Teacher
to
Gordon Smyth
52k
Scholar
to
Aaron Lun
★ 28k
Teacher
to
Michael Love
43k
Popular Question
to
Dario Strbenac
★ 1.5k
Locations
• All
WEHI, Melbourne, Australia,
6 minutes ago
United Kingdom,
14 minutes ago
India,
21 minutes ago
UPF, Barcelona, Spain,
31 minutes ago
Australia,
58 minutes ago
Traffic: 686 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6