Showing : lrt • reset
0
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4
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358
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Extract LRT results for each comparison
LRT DESeq2
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
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3
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917
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Interpretation of LRT results
DESeq2 LRT Heatmap
updated 6 months ago by 65k • written 17 months ago by ▴ 10
0
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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 • 0 • written 6.1 years ago by ▴ 30
0
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7
replies
1.4k
views
LRT test followed by filtering based on LFC
deseq2 LFC LRT
written 5.2 years ago by • 0
1
vote
3
replies
1.3k
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 14 months ago by • 0 • written 2.2 years ago by • 0
0
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1
reply
545
views
DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2 LRT continuous coeficients
updated 15 months ago by 41k • written 15 months ago by ▴ 10
0
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1
reply
672
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2 LRT multifactorial up/down-reg log2FC
updated 16 months ago by 65k • written 16 months ago by ▴ 10
0
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2
replies
746
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Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2 adjp Volcano LRT
written 17 months ago by ▴ 10
4
votes
7
replies
7.6k
views
DESeq2: likelihood ratio test interpretation, multifactor
likelihood ratio test deseq2 LRT
updated 18 months ago by 41k • written 5.7 years ago by ▴ 10
0
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1
reply
547
views
DESeq2 LRT not returning genes
LRT linearmodels DESeq2
updated 21 months ago by 41k • written 21 months ago by ▴ 30
5
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2
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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 • 0 • written 6.6 years ago by • 0
1
vote
11
replies
4.3k
views
Time-series Analysis using DESeq2 and LRT test
deseq2 LRT timecourse
updated 2.1 years ago by 41k • written 7.2 years ago by ★ 1.5k
0
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1
reply
703
views
LRT test in DESeq2 decide on the level of comparisons
DESeq2 LRT Model
updated 2.1 years ago by 41k • written 2.1 years ago by • 0
0
votes
1
reply
780
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
0
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3
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877
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
0
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1
reply
1.7k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
4
votes
18
replies
6.0k
views
DESeq2 - multifactorial design
LRT DESeq2 interaction
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by ▴ 10
1
vote
7
replies
952
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
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4
replies
1.9k
views
Issues with DESeq2 LRT for time-course experiment
rna-seq R DESeq2 LRT
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by ▴ 10
0
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3
replies
618
views
Error using DESeq2's nbinomLRT
deseq2 LRT
updated 3.7 years ago by 41k • written 3.7 years ago by ▴ 20
0
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1
reply
655
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
updated 3.7 years ago by 41k • written 3.7 years ago by ▴ 30
1
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2
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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 41k • written 3.8 years ago by • 0
0
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8
replies
2.5k
views
DESeq LRT reduced model
deseq2 LRT
updated 4.1 years ago by 41k • written 4.1 years ago by • 0
1
vote
1
reply
692
views
multifactor desing with interaction LRT or Wald test?
deseq2 LRT wald
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by ▴ 10
0
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2
replies
952
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 4.3 years ago by 41k • written 4.3 years ago by • 0
2
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2
replies
3.9k
views
understanding edgeR glmLRT
edger lrt
updated 4.4 years ago by 50k • written 4.4 years ago by • 0
1
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1
reply
1.8k
views
DESeq2 test LRT or WALD
deseq2 LRT WALD
updated 4.7 years ago by 41k • written 4.7 years ago by • 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 41k • written 5.1 years ago by • 0
3
votes
3
replies
829
views
clarification of time-series analysis
deseq2 baseline LRT
updated 5.2 years ago by 41k • written 5.2 years ago by ★ 1.5k
0
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4
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1.2k
views
DESeq2 Ribosome Profiling Time-series: Significantly Different Results for Wald and LRT test
deseq2 ribosome profiling wald lrt
updated 5.3 years ago by 41k • written 5.3 years ago by ▴ 20
1
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5
replies
1.4k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 5.4 years ago by 41k • written 5.4 years ago by • 0
1
vote
4
replies
903
views
model for LRT
deseq2 LRT
updated 5.4 years ago by 41k • written 5.4 years ago by • 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 5.4 years ago by • 0 • written 7.0 years ago by ▴ 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 41k • written 5.6 years ago by • 0
2
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4
replies
1.2k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
5.6 years ago Maithê Barros ▴ 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
1
vote
2
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890
views
Interpretation of results names after LRT
DESeq2 LRT multiple time points
updated 6.1 years ago by 41k • written 6.1 years ago by ▴ 40
0
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3
replies
1.2k
views
Error in DESeq "object" not found
deseq2 LRT reduced model
updated 6.2 years ago by 65k • written 6.2 years ago by ▴ 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
6.2 years ago A ▴ 40
0
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4
replies
1.1k
views
Design for DESeq2
LRT deseq2 multiple factor design
6.6 years ago sally_b86 • 0
1
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1
reply
1.2k
views
DESeq2: Is it necessary to include all terms and interactions in LRT tests?
deseq2 lrt
updated 6.6 years ago by ▴ 680 • written 6.6 years ago by • 0
0
votes
6
replies
2.8k
views
DESeq extract result of lrt for a subset of the samples
deseq2 rnaseq lrt
updated 7.0 years ago by 41k • written 7.0 years ago by • 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 ★ 7.9k • written 7.1 years ago by ▴ 20
2
votes
1
reply
1.3k
views
LRT test with or without betaPrior
deseq2 LRT betaprior
updated 7.6 years ago by 41k • written 7.6 years ago by ▴ 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 41k • written 7.9 years ago by ▴ 20
2
votes
5
replies
5.5k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.3 years ago • updated 8.2 years ago rclaire ▴ 20
0
votes
8
replies
2.8k
views
Problems with LRT code using DESeq2
deseq2 LRT differential gene expression
8.4 years ago • updated 8.3 years ago newsomew13 • 0
4
votes
2
replies
9.1k
views
DESeq2 LRT output help
deseq2 LRT anova
8.9 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 41k • written 9.1 years ago by ▴ 90
49 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Votes
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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