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LRT
•
reset
4
votes
2
replies
9.1k
views
DESeq2 LRT output help
deseq2
LRT
anova
8.9 years ago
rclaire
▴ 20
7
votes
7
replies
8.6k
views
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2
LRT
rnaseq
design
reduced model
updated 5.3 years ago by
evocanres
• 0 • written 6.9 years ago by
I.Castanho
▴ 50
4
votes
7
replies
7.5k
views
DESeq2: likelihood ratio test interpretation, multifactor
likelihood ratio test
deseq2
LRT
updated 17 months ago by
Michael Love
41k • written 5.6 years ago by
agdif
▴ 10
8
votes
2
replies
5.9k
views
interpreting LRT results DESeq2
deseq2
LRT
RNA-Seq
updated 9.0 years ago by
Michael Love
41k • written 9.0 years ago by
solgakar@bi.technion.ac.il
▴ 90
4
votes
18
replies
5.8k
views
DESeq2 - multifactorial design
LRT
DESeq2
interaction
updated 3.0 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
annamariabugaj
▴ 10
2
votes
5
replies
5.4k
views
DESeq2 multifactor experiment design
deseq2
LRT
multifactor
contrast
interactions
8.2 years ago
rclaire
▴ 20
1
vote
11
replies
4.2k
views
Time-series Analysis using DESeq2 and LRT test
deseq2
LRT
timecourse
updated 2.0 years ago by
Michael Love
41k • written 7.1 years ago by
Assa Yeroslaviz
★ 1.5k
5
votes
2
replies
4.0k
views
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq
deseq2
lrt
wald
differential gene expression
updated 2.0 years ago by
krushnach80
• 0 • written 6.5 years ago by
chrysanthi.taxiarchi12
• 0
2
votes
2
replies
3.7k
views
understanding edgeR glmLRT
edger
lrt
updated 4.3 years ago by
Gordon Smyth
50k • written 4.3 years ago by
arubio
• 0
0
votes
8
replies
2.8k
views
Problems with LRT code using DESeq2
deseq2
LRT
differential gene expression
8.3 years ago • updated 8.2 years ago
newsomew13
• 0
0
votes
6
replies
2.8k
views
DESeq extract result of lrt for a subset of the samples
deseq2
rnaseq
lrt
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
md27
• 0
0
votes
3
replies
2.6k
views
Wald vs LRT: different number of significant genes when testing the same coefficient
deseq2
wald
lrt
genes
significance
updated 7.8 years ago by
Michael Love
41k • written 7.8 years ago by
aziza
▴ 20
0
votes
8
replies
2.5k
views
DESeq LRT reduced model
deseq2
LRT
updated 4.0 years ago by
Michael Love
41k • written 4.1 years ago by
bio_inc
• 0
1
vote
2
replies
2.0k
views
DeSEQ2- What is the difference between Gene Clustering and using LRT for Time Series experiment WITHOUT treatments
deseq2
Time Series
Gene Clustering
LRT
ATACseq
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
kaiser.karim
• 0
1
vote
4
replies
1.9k
views
Issues with DESeq2 LRT for time-course experiment
rna-seq
R
DESeq2
LRT
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
luke.briody
▴ 10
0
votes
5
replies
1.8k
views
DESeq LRT test and construction of Co-expression network
LRT
co-expression network
deseq2
time course experiment
network analysis
updated 10 months ago by
Jennifer Dehner
• 0 • written 6.0 years ago by
aishu.jp
▴ 30
1
vote
1
reply
1.8k
views
DESeq2 test LRT or WALD
deseq2
LRT
WALD
updated 4.6 years ago by
Michael Love
41k • written 4.6 years ago by
annesoalvarez
• 0
0
votes
1
reply
1.6k
views
DESeq2 time course and dosage response
LRT
Design
DESeq2
doseResponse
TimeSeriesExperiment
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
Mari
• 0
1
vote
1
reply
1.5k
views
DESeq2 high variance in differential expression results
deseq2
variance
lrt
differential gene expression
updated 7.0 years ago by
Ryan C. Thompson
★ 7.9k • written 7.0 years ago by
rclaire
▴ 20
1
vote
5
replies
1.4k
views
Timecourse gene expression analysis with DESeq2
timecourse
deseq2
multiple factor design
LRT
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
juditkovacsbio
• 0
0
votes
7
replies
1.4k
views
LRT test followed by filtering based on LFC
deseq2
LFC
LRT
written 5.1 years ago by
sally.badawi
• 0
3
votes
8
replies
1.4k
views
Filtering for genes >100 counts after LRT still showing significant genes with genes with 0 counts!
LRT
CPM
lowcountgenes
deseq2
6.1 years ago
A
▴ 40
1
vote
6
replies
1.3k
views
differential expression analysis with big dataset and >500 surrogate variables
SVA
deseq2
differential expression
LRT
5.9 years ago
aec
▴ 90
1
vote
2
replies
1.3k
views
"Error in nbinomLRT(... less than one degree of freedom"... Isolating main and interaction effects with the LRT?
deseq2
main effects
interaction effects
R
lrt
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
laurenjfrazee
• 0
1
vote
3
replies
1.3k
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq
LRT
DESeq2
lfcShrink
updated 13 months ago by
ayabalbaa1990
• 0 • written 2.2 years ago by
Emma
• 0
2
votes
1
reply
1.2k
views
LRT test with or without betaPrior
deseq2
LRT
betaprior
updated 7.5 years ago by
Michael Love
41k • written 7.5 years ago by
laianavarromartin
▴ 20
0
votes
4
replies
1.2k
views
DESeq2 Ribosome Profiling Time-series: Significantly Different Results for Wald and LRT test
deseq2
ribosome profiling
wald
lrt
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
indrik.wijaya
▴ 20
0
votes
3
replies
1.2k
views
Error in DESeq "object" not found
deseq2
LRT
reduced model
updated 6.1 years ago by
James W. MacDonald
65k • written 6.1 years ago by
A
▴ 40
1
vote
1
reply
1.2k
views
DESeq2: Is it necessary to include all terms and interactions in LRT tests?
deseq2
lrt
updated 6.5 years ago by
Gavin Kelly
▴ 680 • written 6.5 years ago by
chimeric
• 0
0
votes
6
replies
1.2k
views
Custom model matrix for multi factordesign
deseq2
LRT
geometric mean
estimatesizefactors
model.matrix
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
carol.brunel
• 0
2
votes
4
replies
1.1k
views
RNA-seq time course experiment - LRT design hep
deseq2
lrt
timecourse
5.5 years ago
Maithê Barros
▴ 10
0
votes
4
replies
1.1k
views
Design for DESeq2
LRT
deseq2
multiple factor design
6.5 years ago
sally_b86
• 0
1
vote
7
replies
926
views
How to get multi-factor Deseq LRT test log P values for a particular condition
Deseq2
LRT
Factors
RNAseq
3.6 years ago
aishu.jp
▴ 30
0
votes
2
replies
912
views
Design of time-course experiment in DESeq2
deseq2
design
design formula
time course
lrt
updated 4.2 years ago by
Michael Love
41k • written 4.2 years ago by
ac_bioinformatics
• 0
1
vote
4
replies
890
views
model for LRT
deseq2
LRT
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
takashi.k1201
• 0
1
vote
2
replies
873
views
Interpretation of results names after LRT
DESeq2
LRT
multiple time points
updated 6.1 years ago by
Michael Love
41k • written 6.1 years ago by
A
▴ 40
0
votes
3
replies
862
views
Interpretation of LRT results
DESeq2
LRT
Heatmap
updated 5 months ago by
James W. MacDonald
65k • written 17 months ago by
Laia
▴ 10
0
votes
3
replies
842
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2
LRT
two-way-ANOVA
interactions
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
Enzo.Scifo
• 0
3
votes
3
replies
819
views
clarification of time-series analysis
deseq2
baseline
LRT
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
744
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome
LRT
DESeq2
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
Mir
• 0
0
votes
2
replies
705
views
Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2
adjp
Volcano
LRT
written 16 months ago by
Laia
▴ 10
0
votes
1
reply
684
views
LRT test in DESeq2 decide on the level of comparisons
DESeq2
LRT
Model
updated 2.0 years ago by
Michael Love
41k • written 2.0 years ago by
JaneDoe
• 0
1
vote
1
reply
670
views
multifactor desing with interaction LRT or Wald test?
deseq2
LRT
wald
updated 4.1 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
jnaviapelaez
▴ 10
0
votes
1
reply
638
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2
LRT
RNAseq
condition
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
aishu.jp
▴ 30
0
votes
1
reply
636
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2
LRT
multifactorial
up/down-reg
log2FC
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
Laia
▴ 10
0
votes
3
replies
601
views
Error using DESeq2's nbinomLRT
deseq2
LRT
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
guyho
▴ 20
0
votes
1
reply
524
views
DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2
LRT
continuous
coeficients
updated 14 months ago by
Michael Love
41k • written 14 months ago by
Laia
▴ 10
0
votes
1
reply
523
views
DESeq2 LRT not returning genes
LRT
linearmodels
DESeq2
updated 20 months ago by
Michael Love
41k • written 20 months ago by
meeta.mistry
▴ 30
0
votes
4
replies
333
views
Extract LRT results for each comparison
LRT
DESeq2
updated 5 months ago by
ATpoint
★ 4.0k • written 5 months ago by
Yijing
• 0
49 results • Page
1 of 1
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
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Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
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James W. MacDonald
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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