Showing : LRT • reset
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 5 months ago by 67k • written 5 months ago by • 0
0
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1
reply
645
views
DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 5 months ago by 43k • written 5 months ago by • 0
0
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4
replies
692
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Extract LRT results for each comparison
LRT DESeq2
updated 15 months ago by ★ 4.6k • written 15 months ago by • 0
0
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7
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1.8k
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LRT test followed by filtering based on LFC
deseq2 LFC LRT
written 5.9 years ago by • 0
0
votes
1
reply
756
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DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2 LRT continuous coeficients
updated 23 months ago by 43k • written 23 months ago by ▴ 10
0
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1
reply
932
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2 LRT multifactorial up/down-reg log2FC
updated 2.0 years ago by 67k • written 2.0 years ago by ▴ 10
0
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2
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1.0k
views
Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2 adjp Volcano LRT
written 2.1 years ago by ▴ 10
1
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3
replies
1.5k
views
Interpretation of LRT results
DESeq2 LRT Heatmap
updated 15 months ago by 67k • written 2.2 years ago by ▴ 10
0
votes
1
reply
716
views
DESeq2 LRT not returning genes
LRT linearmodels DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 30
0
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1
reply
913
views
LRT test in DESeq2 decide on the level of comparisons
DESeq2 LRT Model
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
1
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3
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1.6k
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 23 months ago by • 0 • written 2.9 years ago by • 0
0
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1
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1.1k
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
3
replies
1.2k
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 3.3 years ago by 43k • written 3.4 years ago by • 0
0
votes
1
reply
2.1k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
4
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18
replies
7.6k
views
DESeq2 - multifactorial design
LRT DESeq2 interaction
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by ▴ 10
1
vote
7
replies
1.2k
views
How to get multi-factor Deseq LRT test log P values for a particular condition
Deseq2 LRT Factors RNAseq
4.3 years ago aishu.jp ▴ 30
1
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4
replies
2.2k
views
Issues with DESeq2 LRT for time-course experiment
rna-seq R DESeq2 LRT
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by ▴ 10
0
votes
3
replies
793
views
Error using DESeq2's nbinomLRT
deseq2 LRT
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 30
0
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1
reply
827
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 30
1
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2
replies
1.6k
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 4.5 years ago by 43k • written 4.5 years ago by • 0
0
votes
8
replies
3.0k
views
DESeq LRT reduced model
deseq2 LRT
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
1
vote
1
reply
901
views
multifactor desing with interaction LRT or Wald test?
deseq2 LRT wald
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
2
votes
2
replies
5.1k
views
understanding edgeR glmLRT
edger lrt
updated 5.0 years ago by 52k • written 5.0 years ago by • 0
1
vote
1
reply
2.1k
views
DESeq2 test LRT or WALD
deseq2 LRT WALD
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
1
vote
2
replies
2.3k
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 5.8 years ago by 43k • written 5.8 years ago by • 0
3
votes
3
replies
993
views
clarification of time-series analysis
deseq2 baseline LRT
updated 5.9 years ago by 43k • written 5.9 years ago by ★ 1.5k
0
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4
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1.5k
views
DESeq2 Ribosome Profiling Time-series: Significantly Different Results for Wald and LRT test
deseq2 ribosome profiling wald lrt
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 20
1
vote
5
replies
1.7k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
vote
4
replies
1.1k
views
model for LRT
deseq2 LRT
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
7
votes
7
replies
9.3k
views
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2 LRT rnaseq design reduced model
updated 6.1 years ago by • 0 • written 7.7 years ago by ▴ 50
0
votes
6
replies
1.4k
views
Custom model matrix for multi factordesign
deseq2 LRT geometric mean estimatesizefactors model.matrix
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
2
votes
4
replies
1.4k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
6.3 years ago Maithê Barros ▴ 10
4
votes
7
replies
8.7k
views
DESeq2: likelihood ratio test interpretation, multifactor
likelihood ratio test deseq2 LRT
updated 2.2 years ago by 43k • written 6.4 years ago by ▴ 10
1
vote
6
replies
1.5k
views
differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
6.6 years ago aec ▴ 90
0
votes
5
replies
2.2k
views
DESeq LRT test and construction of Co-expression network
LRT co-expression network deseq2 time course experiment network analysis
updated 19 months ago by • 0 • written 6.8 years ago by ▴ 30
1
vote
2
replies
1.1k
views
Interpretation of results names after LRT
DESeq2 LRT multiple time points
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 40
0
votes
3
replies
1.6k
views
Error in DESeq "object" not found
deseq2 LRT reduced model
updated 6.8 years ago by 67k • written 6.8 years ago by ▴ 40
3
votes
8
replies
1.7k
views
Filtering for genes >100 counts after LRT still showing significant genes with genes with 0 counts!
LRT CPM lowcountgenes deseq2
6.9 years ago A ▴ 40
0
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4
replies
1.3k
views
Design for DESeq2
LRT deseq2 multiple factor design
7.2 years ago sally_b86 • 0
2
votes
1
reply
1.5k
views
DESeq2: Is it necessary to include all terms and interactions in LRT tests?
deseq2 lrt
updated 7.3 years ago by ▴ 690 • written 7.3 years ago by • 0
5
votes
2
replies
4.3k
views
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 lrt wald differential gene expression
updated 2.8 years ago by • 0 • written 7.3 years ago by • 0
0
votes
6
replies
3.2k
views
DESeq extract result of lrt for a subset of the samples
deseq2 rnaseq lrt
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
1
vote
1
reply
1.8k
views
DESeq2 high variance in differential expression results
deseq2 variance lrt differential gene expression
updated 7.7 years ago by ★ 7.9k • written 7.7 years ago by ▴ 20
1
vote
11
replies
4.8k
views
Time-series Analysis using DESeq2 and LRT test
deseq2 LRT timecourse
updated 2.8 years ago by 43k • written 7.9 years ago by ★ 1.5k
2
votes
1
reply
1.5k
views
LRT test with or without betaPrior
deseq2 LRT betaprior
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 20
0
votes
3
replies
2.9k
views
Wald vs LRT: different number of significant genes when testing the same coefficient
deseq2 wald lrt genes significance
updated 8.5 years ago by 43k • written 8.5 years ago by ▴ 20
2
votes
5
replies
5.9k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.9 years ago rclaire ▴ 20
0
votes
8
replies
3.2k
views
Problems with LRT code using DESeq2
deseq2 LRT differential gene expression
9.1 years ago • updated 9.0 years ago newsomew13 • 0
4
votes
2
replies
9.5k
views
DESeq2 LRT output help
deseq2 LRT anova
9.6 years ago rclaire ▴ 20
50 results • Page 1 of 1
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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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