Showing : LRT • reset
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 4 months ago by 67k • written 4 months ago by • 0
0
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1
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616
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 4 months ago by 43k • written 4 months ago by • 0
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4
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672
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Extract LRT results for each comparison
LRT DESeq2
updated 14 months ago by ★ 4.6k • written 14 months ago by • 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 5.8 years ago by • 0
0
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1
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738
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DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2 LRT continuous coeficients
updated 22 months ago by 43k • written 22 months ago by ▴ 10
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1
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909
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Log2FC in LRT vs Wald in multifactorial design
DESeq2 LRT multifactorial up/down-reg log2FC
updated 24 months ago by 67k • written 24 months ago by ▴ 10
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2
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1.0k
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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
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3
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1.4k
views
Interpretation of LRT results
DESeq2 LRT Heatmap
updated 14 months ago by 67k • written 2.1 years ago by ▴ 10
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1
reply
702
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DESeq2 LRT not returning genes
LRT linearmodels DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 30
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1
reply
898
views
LRT test in DESeq2 decide on the level of comparisons
DESeq2 LRT Model
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
1
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3
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1.6k
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Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 22 months ago by • 0 • written 2.9 years ago by • 0
0
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1
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1.0k
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
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3
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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 3.3 years ago by • 0
0
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1
reply
2.1k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
4
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18
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7.4k
views
DESeq2 - multifactorial design
LRT DESeq2 interaction
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by ▴ 10
1
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7
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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
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3
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776
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Error using DESeq2's nbinomLRT
deseq2 LRT
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 30
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1
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813
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How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 30
1
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2
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1.5k
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 4.4 years ago by 43k • written 4.4 years ago by • 0
0
votes
8
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3.0k
views
DESeq LRT reduced model
deseq2 LRT
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
1
vote
1
reply
888
views
multifactor desing with interaction LRT or Wald test?
deseq2 LRT wald
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 10
0
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2
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1.3k
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
2
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2
replies
5.0k
views
understanding edgeR glmLRT
edger lrt
updated 5.0 years ago by 52k • written 5.0 years ago by • 0
1
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1
reply
2.1k
views
DESeq2 test LRT or WALD
deseq2 LRT WALD
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
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2
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2.2k
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
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3
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979
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clarification of time-series analysis
deseq2 baseline LRT
updated 5.8 years ago by 43k • written 5.8 years ago by ★ 1.5k
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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 5.9 years ago by 43k • written 5.9 years ago by ▴ 20
1
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5
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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
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4
replies
1.1k
views
model for LRT
deseq2 LRT
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
7
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7
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9.1k
views
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2 LRT rnaseq design reduced model
updated 6.0 years ago by • 0 • written 7.6 years ago by ▴ 50
0
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6
replies
1.4k
views
Custom model matrix for multi factordesign
deseq2 LRT geometric mean estimatesizefactors model.matrix
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
2
votes
4
replies
1.4k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
6.2 years ago Maithê Barros ▴ 10
4
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7
replies
8.5k
views
DESeq2: likelihood ratio test interpretation, multifactor
likelihood ratio test deseq2 LRT
updated 2.1 years ago by 43k • written 6.3 years ago by ▴ 10
1
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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
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5
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2.2k
views
DESeq LRT test and construction of Co-expression network
LRT co-expression network deseq2 time course experiment network analysis
updated 18 months ago by • 0 • written 6.7 years ago by ▴ 30
1
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2
replies
1.1k
views
Interpretation of results names after LRT
DESeq2 LRT multiple time points
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 40
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3
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1.5k
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
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8
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1.6k
views
Filtering for genes >100 counts after LRT still showing significant genes with genes with 0 counts!
LRT CPM lowcountgenes deseq2
6.8 years ago A ▴ 40
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4
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1.3k
views
Design for DESeq2
LRT deseq2 multiple factor design
7.2 years ago sally_b86 • 0
2
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1
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1.5k
views
DESeq2: Is it necessary to include all terms and interactions in LRT tests?
deseq2 lrt
updated 7.2 years ago by ▴ 690 • written 7.2 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 2.7 years ago by • 0 • written 7.2 years ago by • 0
0
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6
replies
3.1k
views
DESeq extract result of lrt for a subset of the samples
deseq2 rnaseq lrt
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
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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 2.7 years ago by 43k • written 7.8 years ago by ★ 1.5k
2
votes
1
reply
1.5k
views
LRT test with or without betaPrior
deseq2 LRT betaprior
updated 8.2 years ago by 43k • written 8.2 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 • updated 8.8 years ago rclaire ▴ 20
0
votes
8
replies
3.1k
views
Problems with LRT code using DESeq2
deseq2 LRT differential gene expression
9.0 years ago • updated 8.9 years ago newsomew13 • 0
4
votes
2
replies
9.5k
views
DESeq2 LRT output help
deseq2 LRT anova
9.5 years ago rclaire ▴ 20
50 results • Page 1 of 1
Recent ...
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Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd by liu.n • 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0
> dim(spe) [1] 19962 425
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Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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