Showing : LRT • reset
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 8 months ago by 68k • written 8 months ago by • 0
0
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1
reply
780
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 8 months ago by 43k • written 8 months ago by • 0
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4
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825
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Extract LRT results for each comparison
LRT DESeq2
updated 18 months ago by ★ 4.8k • written 18 months ago by • 0
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7
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LRT test followed by filtering based on LFC
deseq2 LFC LRT
written 6.1 years ago by • 0
0
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1
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858
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DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2 LRT continuous coeficients
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 10
0
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1
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1.0k
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Log2FC in LRT vs Wald in multifactorial design
DESeq2 LRT multifactorial up/down-reg log2FC
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
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2
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1.1k
views
Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2 adjp Volcano LRT
written 2.4 years ago by ▴ 10
1
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3
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1.8k
views
Interpretation of LRT results
DESeq2 LRT Heatmap
updated 18 months ago by 68k • written 2.4 years ago by ▴ 10
0
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1
reply
771
views
DESeq2 LRT not returning genes
LRT linearmodels DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 30
0
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1
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964
views
LRT test in DESeq2 decide on the level of comparisons
DESeq2 LRT Model
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
1
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3
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1.8k
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Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 2.2 years ago by • 0 • written 3.2 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 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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3
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1.3k
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
votes
1
reply
2.4k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
4
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18
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8.3k
views
DESeq2 - multifactorial design
LRT DESeq2 interaction
updated 4.0 years ago by ★ 4.0k • written 4.1 years ago by ▴ 10
1
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7
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1.3k
views
How to get multi-factor Deseq LRT test log P values for a particular condition
Deseq2 LRT Factors RNAseq
4.6 years ago aishu.jp ▴ 30
1
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4
replies
2.3k
views
Issues with DESeq2 LRT for time-course experiment
rna-seq R DESeq2 LRT
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by ▴ 10
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3
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889
views
Error using DESeq2's nbinomLRT
deseq2 LRT
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 30
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1
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866
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 30
1
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2
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1.7k
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 4.8 years ago by 43k • written 4.8 years ago by • 0
0
votes
8
replies
3.2k
views
DESeq LRT reduced model
deseq2 LRT
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
1
vote
1
reply
980
views
multifactor desing with interaction LRT or Wald test?
deseq2 LRT wald
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by ▴ 10
0
votes
2
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1.4k
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
2
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2
replies
5.6k
views
understanding edgeR glmLRT
edger lrt
updated 5.3 years ago by 52k • written 5.3 years ago by • 0
1
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1
reply
2.2k
views
DESeq2 test LRT or WALD
deseq2 LRT WALD
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
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2
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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 6.1 years ago by 43k • written 6.1 years ago by • 0
3
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3
replies
1.1k
views
clarification of time-series analysis
deseq2 baseline LRT
updated 6.1 years ago by 43k • written 6.1 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 6.3 years ago by 43k • written 6.3 years ago by ▴ 20
1
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5
replies
1.9k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
1
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4
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1.2k
views
model for LRT
deseq2 LRT
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
7
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7
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9.4k
views
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2 LRT rnaseq design reduced model
updated 6.3 years ago by • 0 • written 7.9 years ago by ▴ 50
0
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6
replies
1.5k
views
Custom model matrix for multi factordesign
deseq2 LRT geometric mean estimatesizefactors model.matrix
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
votes
4
replies
1.5k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
6.6 years ago Maithê Barros ▴ 10
4
votes
7
replies
9.2k
views
DESeq2: likelihood ratio test interpretation, multifactor
likelihood ratio test deseq2 LRT
updated 2.5 years ago by 43k • written 6.7 years ago by ▴ 10
1
vote
6
replies
1.6k
views
differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
6.9 years ago aec ▴ 90
0
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5
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2.3k
views
DESeq LRT test and construction of Co-expression network
LRT co-expression network deseq2 time course experiment network analysis
updated 22 months ago by • 0 • written 7.1 years ago by ▴ 30
1
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2
replies
1.2k
views
Interpretation of results names after LRT
DESeq2 LRT multiple time points
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 60
0
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3
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1.8k
views
Error in DESeq "object" not found
deseq2 LRT reduced model
updated 7.1 years ago by 68k • written 7.1 years ago by ▴ 60
3
votes
8
replies
1.8k
views
Filtering for genes >100 counts after LRT still showing significant genes with genes with 0 counts!
LRT CPM lowcountgenes deseq2
7.2 years ago A ▴ 60
0
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4
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1.3k
views
Design for DESeq2
LRT deseq2 multiple factor design
7.5 years ago sally_b86 • 0
2
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1
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1.6k
views
DESeq2: Is it necessary to include all terms and interactions in LRT tests?
deseq2 lrt
updated 7.6 years ago by ▴ 690 • written 7.6 years ago by • 0
5
votes
2
replies
4.5k
views
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 lrt wald differential gene expression
updated 3.0 years ago by • 0 • written 7.6 years ago by • 0
0
votes
6
replies
3.3k
views
DESeq extract result of lrt for a subset of the samples
deseq2 rnaseq lrt
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
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1
reply
1.9k
views
DESeq2 high variance in differential expression results
deseq2 variance lrt differential gene expression
updated 8.0 years ago by ★ 7.9k • written 8.0 years ago by ▴ 20
1
vote
11
replies
5.0k
views
Time-series Analysis using DESeq2 and LRT test
deseq2 LRT timecourse
updated 3.0 years ago by 43k • written 8.2 years ago by ★ 1.5k
2
votes
1
reply
1.5k
views
LRT test with or without betaPrior
deseq2 LRT betaprior
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 20
0
votes
3
replies
3.0k
views
Wald vs LRT: different number of significant genes when testing the same coefficient
deseq2 wald lrt genes significance
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 20
2
votes
5
replies
6.0k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
9.2 years ago rclaire ▴ 20
0
votes
8
replies
3.3k
views
Problems with LRT code using DESeq2
deseq2 LRT differential gene expression
9.4 years ago • updated 9.2 years ago newsomew13 • 0
4
votes
2
replies
9.7k
views
DESeq2 LRT output help
deseq2 LRT anova
9.9 years ago rclaire ▴ 20
50 results • Page 1 of 1
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Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…
Answer: DESeq2 - am I extracting results incorrectly? by James W. MacDonald 68k
If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…
Answer: Origin of the labels for the SingleCellMultiModal dataset by ATpoint ★ 4.8k
If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by ATpoint ★ 4.8k
That plot looks extremely worrying. You have very unbalanced DE profiles and clearly two populations of peaks on the right. I would make su…
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Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Answer: SingleR with multiple single cell references
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