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LRT
•
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0
votes
4
replies
399
views
Extract LRT results for each comparison
LRT
DESeq2
updated 7 months ago by
ATpoint
★ 4.1k • written 7 months ago by
Yijing
• 0
0
votes
7
replies
1.5k
views
LRT test followed by filtering based on LFC
deseq2
LFC
LRT
written 5.3 years ago by
sally.badawi
• 0
0
votes
1
reply
562
views
DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2
LRT
continuous
coeficients
updated 15 months ago by
Michael Love
42k • written 15 months ago by
Laia
▴ 10
0
votes
1
reply
691
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2
LRT
multifactorial
up/down-reg
log2FC
updated 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Laia
▴ 10
0
votes
2
replies
777
views
Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2
adjp
Volcano
LRT
written 18 months ago by
Laia
▴ 10
0
votes
3
replies
968
views
Interpretation of LRT results
DESeq2
LRT
Heatmap
updated 7 months ago by
James W. MacDonald
65k • written 18 months ago by
Laia
▴ 10
0
votes
1
reply
566
views
DESeq2 LRT not returning genes
LRT
linearmodels
DESeq2
updated 22 months ago by
Michael Love
42k • written 22 months ago by
meeta.mistry
▴ 30
0
votes
1
reply
727
views
LRT test in DESeq2 decide on the level of comparisons
DESeq2
LRT
Model
updated 2.2 years ago by
Michael Love
42k • written 2.2 years ago by
JaneDoe
• 0
1
vote
3
replies
1.3k
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq
LRT
DESeq2
lfcShrink
updated 15 months ago by
ayabalbaa1990
• 0 • written 2.3 years ago by
Emma
• 0
0
votes
1
reply
823
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome
LRT
DESeq2
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
Mir
• 0
0
votes
3
replies
918
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2
LRT
two-way-ANOVA
interactions
updated 2.7 years ago by
Michael Love
42k • written 2.7 years ago by
Enzo.Scifo
• 0
0
votes
1
reply
1.7k
views
DESeq2 time course and dosage response
LRT
Design
DESeq2
doseResponse
TimeSeriesExperiment
updated 2.8 years ago by
Michael Love
42k • written 2.8 years ago by
Mari
• 0
4
votes
18
replies
6.2k
views
DESeq2 - multifactorial design
LRT
DESeq2
interaction
updated 3.2 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
annamariabugaj
▴ 10
1
vote
7
replies
972
views
How to get multi-factor Deseq LRT test log P values for a particular condition
Deseq2
LRT
Factors
RNAseq
3.7 years ago
aishu.jp
▴ 30
1
vote
4
replies
1.9k
views
Issues with DESeq2 LRT for time-course experiment
rna-seq
R
DESeq2
LRT
updated 3.7 years ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
luke.briody
▴ 10
0
votes
3
replies
633
views
Error using DESeq2's nbinomLRT
deseq2
LRT
updated 3.8 years ago by
Michael Love
42k • written 3.8 years ago by
guyho
▴ 20
0
votes
1
reply
667
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2
LRT
RNAseq
condition
updated 3.8 years ago by
Michael Love
42k • written 3.8 years ago by
aishu.jp
▴ 30
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 3.9 years ago by
Michael Love
42k • written 3.9 years ago by
laurenjfrazee
• 0
0
votes
8
replies
2.6k
views
DESeq LRT reduced model
deseq2
LRT
updated 4.2 years ago by
Michael Love
42k • written 4.2 years ago by
bio_inc
• 0
1
vote
1
reply
715
views
multifactor desing with interaction LRT or Wald test?
deseq2
LRT
wald
updated 4.2 years ago by
Kevin Blighe
★ 3.9k • written 4.2 years ago by
jnaviapelaez
▴ 10
0
votes
2
replies
996
views
Design of time-course experiment in DESeq2
deseq2
design
design formula
time course
lrt
updated 4.3 years ago by
Michael Love
42k • written 4.3 years ago by
ac_bioinformatics
• 0
2
votes
2
replies
4.0k
views
understanding edgeR glmLRT
edger
lrt
updated 4.4 years ago by
Gordon Smyth
50k • written 4.4 years ago by
arubio
• 0
1
vote
1
reply
1.9k
views
DESeq2 test LRT or WALD
deseq2
LRT
WALD
updated 4.8 years ago by
Michael Love
42k • written 4.8 years ago by
annesoalvarez
• 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 5.2 years ago by
Michael Love
42k • written 5.2 years ago by
kaiser.karim
• 0
3
votes
3
replies
843
views
clarification of time-series analysis
deseq2
baseline
LRT
updated 5.2 years ago by
Michael Love
42k • written 5.2 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
4
replies
1.3k
views
DESeq2 Ribosome Profiling Time-series: Significantly Different Results for Wald and LRT test
deseq2
ribosome profiling
wald
lrt
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
indrik.wijaya
▴ 20
1
vote
5
replies
1.5k
views
Timecourse gene expression analysis with DESeq2
timecourse
deseq2
multiple factor design
LRT
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
juditkovacsbio
• 0
1
vote
4
replies
918
views
model for LRT
deseq2
LRT
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
takashi.k1201
• 0
7
votes
7
replies
8.7k
views
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2
LRT
rnaseq
design
reduced model
updated 5.5 years ago by
evocanres
• 0 • written 7.0 years ago by
I.Castanho
▴ 50
0
votes
6
replies
1.2k
views
Custom model matrix for multi factordesign
deseq2
LRT
geometric mean
estimatesizefactors
model.matrix
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
carol.brunel
• 0
2
votes
4
replies
1.2k
views
RNA-seq time course experiment - LRT design hep
deseq2
lrt
timecourse
5.7 years ago
Maithê Barros
▴ 10
4
votes
7
replies
7.7k
views
DESeq2: likelihood ratio test interpretation, multifactor
likelihood ratio test
deseq2
LRT
updated 19 months ago by
Michael Love
42k • written 5.8 years ago by
agdif
▴ 10
1
vote
6
replies
1.3k
views
differential expression analysis with big dataset and >500 surrogate variables
SVA
deseq2
differential expression
LRT
6.0 years ago
aec
▴ 90
0
votes
5
replies
1.9k
views
DESeq LRT test and construction of Co-expression network
LRT
co-expression network
deseq2
time course experiment
network analysis
updated 11 months ago by
Jennifer Dehner
• 0 • written 6.2 years ago by
aishu.jp
▴ 30
1
vote
2
replies
905
views
Interpretation of results names after LRT
DESeq2
LRT
multiple time points
updated 6.2 years ago by
Michael Love
42k • written 6.2 years ago by
A
▴ 40
0
votes
3
replies
1.3k
views
Error in DESeq "object" not found
deseq2
LRT
reduced model
updated 6.2 years ago by
James W. MacDonald
65k • written 6.2 years ago by
A
▴ 40
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
6.3 years ago
A
▴ 40
0
votes
4
replies
1.1k
views
Design for DESeq2
LRT
deseq2
multiple factor design
6.6 years ago
sally_b86
• 0
1
vote
1
reply
1.2k
views
DESeq2: Is it necessary to include all terms and interactions in LRT tests?
deseq2
lrt
updated 6.7 years ago by
Gavin Kelly
▴ 680 • written 6.7 years ago by
chimeric
• 0
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 2.1 years ago by
krushnach80
• 0 • written 6.7 years ago by
chrysanthi.taxiarchi12
• 0
0
votes
6
replies
2.9k
views
DESeq extract result of lrt for a subset of the samples
deseq2
rnaseq
lrt
updated 7.1 years ago by
Michael Love
42k • written 7.1 years ago by
md27
• 0
1
vote
1
reply
1.5k
views
DESeq2 high variance in differential expression results
deseq2
variance
lrt
differential gene expression
updated 7.1 years ago by
Ryan C. Thompson
★ 7.9k • written 7.1 years ago by
rclaire
▴ 20
1
vote
11
replies
4.3k
views
Time-series Analysis using DESeq2 and LRT test
deseq2
LRT
timecourse
updated 2.2 years ago by
Michael Love
42k • written 7.3 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
1
reply
1.3k
views
LRT test with or without betaPrior
deseq2
LRT
betaprior
updated 7.7 years ago by
Michael Love
42k • written 7.7 years ago by
laianavarromartin
▴ 20
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 7.9 years ago by
Michael Love
42k • written 7.9 years ago by
aziza
▴ 20
2
votes
5
replies
5.5k
views
DESeq2 multifactor experiment design
deseq2
LRT
multifactor
contrast
interactions
8.3 years ago
rclaire
▴ 20
0
votes
8
replies
2.9k
views
Problems with LRT code using DESeq2
deseq2
LRT
differential gene expression
8.5 years ago • updated 8.4 years ago
newsomew13
• 0
4
votes
2
replies
9.2k
views
DESeq2 LRT output help
deseq2
LRT
anova
9.0 years ago
rclaire
▴ 20
8
votes
2
replies
6.0k
views
interpreting LRT results DESeq2
deseq2
LRT
RNA-Seq
updated 9.1 years ago by
Michael Love
42k • written 9.1 years ago by
solgakar@bi.technion.ac.il
▴ 90
49 results • Page
1 of 1
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Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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