Showing : lrt • reset
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 13 months ago by 68k • written 13 months ago by • 0
0
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1
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924
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 13 months ago by 43k • written 13 months ago by • 0
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4
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951
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Extract LRT results for each comparison
LRT DESeq2
updated 23 months ago by ★ 4.9k • written 23 months ago by • 0
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7
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2.1k
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LRT test followed by filtering based on LFC
deseq2 LFC LRT
written 6.5 years ago by • 0
0
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1
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949
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DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2 LRT continuous coeficients
updated 2.6 years ago by 43k • written 2.6 years ago by ▴ 10
0
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1
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1.1k
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Log2FC in LRT vs Wald in multifactorial design
DESeq2 LRT multifactorial up/down-reg log2FC
updated 2.7 years ago by 68k • written 2.7 years ago by ▴ 10
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2
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1.3k
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Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2 adjp Volcano LRT
written 2.8 years ago by ▴ 10
1
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3
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2.0k
views
Interpretation of LRT results
DESeq2 LRT Heatmap
updated 23 months ago by 68k • written 2.8 years ago by ▴ 10
0
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1
reply
841
views
DESeq2 LRT not returning genes
LRT linearmodels DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 30
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1
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1.0k
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LRT test in DESeq2 decide on the level of comparisons
DESeq2 LRT Model
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
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3
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Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 2.6 years ago by • 0 • written 3.6 years ago by • 0
0
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1
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1.2k
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DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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3
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1.4k
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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1
reply
2.6k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
4
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18
replies
8.8k
views
DESeq2 - multifactorial design
LRT DESeq2 interaction
updated 4.4 years ago by ★ 4.0k • written 4.5 years ago by ▴ 10
1
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7
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1.4k
views
How to get multi-factor Deseq LRT test log P values for a particular condition
Deseq2 LRT Factors RNAseq
5.0 years ago aishu.jp ▴ 30
1
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4
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2.4k
views
Issues with DESeq2 LRT for time-course experiment
rna-seq R DESeq2 LRT
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by ▴ 10
0
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3
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1.0k
views
Error using DESeq2's nbinomLRT
deseq2 LRT
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 30
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1
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1.0k
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 30
1
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2
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1.8k
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 5.2 years ago by 43k • written 5.2 years ago by • 0
0
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8
replies
3.4k
views
DESeq LRT reduced model
deseq2 LRT
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
1
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1
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1.0k
views
multifactor desing with interaction LRT or Wald test?
deseq2 LRT wald
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
0
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2
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1.6k
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
2
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2
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6.0k
views
understanding edgeR glmLRT
edger lrt
updated 5.7 years ago by 52k • written 5.7 years ago by • 0
1
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1
reply
2.3k
views
DESeq2 test LRT or WALD
deseq2 LRT WALD
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
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2
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2.5k
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 6.5 years ago by 43k • written 6.5 years ago by • 0
3
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3
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1.2k
views
clarification of time-series analysis
deseq2 baseline LRT
updated 6.5 years ago by 43k • written 6.5 years ago by ★ 1.5k
0
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4
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1.6k
views
DESeq2 Ribosome Profiling Time-series: Significantly Different Results for Wald and LRT test
deseq2 ribosome profiling wald lrt
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 20
1
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5
replies
2.0k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
1
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4
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1.3k
views
model for LRT
deseq2 LRT
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
7
votes
7
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9.7k
views
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2 LRT rnaseq design reduced model
updated 6.8 years ago by • 0 • written 8.3 years ago by ▴ 50
0
votes
6
replies
1.6k
views
Custom model matrix for multi factordesign
deseq2 LRT geometric mean estimatesizefactors model.matrix
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
2
votes
4
replies
1.7k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
7.0 years ago Maithê Barros ▴ 10
4
votes
7
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9.5k
views
DESeq2: likelihood ratio test interpretation, multifactor
likelihood ratio test deseq2 LRT
updated 2.9 years ago by 43k • written 7.1 years ago by ▴ 10
1
vote
6
replies
1.8k
views
differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
7.3 years ago aec ▴ 90
0
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5
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2.4k
views
DESeq LRT test and construction of Co-expression network
LRT co-expression network deseq2 time course experiment network analysis
updated 2.3 years ago by • 0 • written 7.5 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 7.5 years ago by 43k • written 7.5 years ago by ▴ 60
0
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3
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2.0k
views
Error in DESeq "object" not found
deseq2 LRT reduced model
updated 7.5 years ago by 68k • written 7.5 years ago by ▴ 60
3
votes
8
replies
1.9k
views
Filtering for genes >100 counts after LRT still showing significant genes with genes with 0 counts!
LRT CPM lowcountgenes deseq2
7.6 years ago A ▴ 60
0
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4
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1.4k
views
Design for DESeq2
LRT deseq2 multiple factor design
7.9 years ago sally_b86 • 0
2
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1
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1.8k
views
DESeq2: Is it necessary to include all terms and interactions in LRT tests?
deseq2 lrt
updated 8.0 years ago by ▴ 690 • written 8.0 years ago by • 0
5
votes
2
replies
4.6k
views
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 lrt wald differential gene expression
updated 3.4 years ago by • 0 • written 8.0 years ago by • 0
0
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6
replies
3.4k
views
DESeq extract result of lrt for a subset of the samples
deseq2 rnaseq lrt
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
1
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1
reply
2.0k
views
DESeq2 high variance in differential expression results
deseq2 variance lrt differential gene expression
updated 8.4 years ago by ★ 7.9k • written 8.4 years ago by ▴ 20
1
vote
11
replies
5.2k
views
Time-series Analysis using DESeq2 and LRT test
deseq2 LRT timecourse
updated 3.4 years ago by 43k • written 8.6 years ago by ★ 1.5k
2
votes
1
reply
1.6k
views
LRT test with or without betaPrior
deseq2 LRT betaprior
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 20
0
votes
3
replies
3.1k
views
Wald vs LRT: different number of significant genes when testing the same coefficient
deseq2 wald lrt genes significance
updated 9.2 years ago by 43k • written 9.2 years ago by ▴ 20
2
votes
5
replies
6.1k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
9.6 years ago rclaire ▴ 20
0
votes
8
replies
3.4k
views
Problems with LRT code using DESeq2
deseq2 LRT differential gene expression
9.8 years ago • updated 9.6 years ago newsomew13 • 0
4
votes
2
replies
9.8k
views
DESeq2 LRT output help
deseq2 LRT anova
10.3 years ago rclaire ▴ 20
51 results • Page 1 of 2
Recent ...
Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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