Showing : lrt • reset
0
votes
8
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2.9k
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Problems with LRT code using DESeq2
deseq2 LRT differential gene expression
8.5 years ago • updated 8.3 years ago newsomew13 • 0
2
votes
5
replies
5.5k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.3 years ago rclaire ▴ 20
1
vote
7
replies
969
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
4
votes
18
replies
6.1k
views
DESeq2 - multifactorial design
LRT DESeq2 interaction
updated 3.1 years ago by ★ 3.9k • written 3.2 years ago by ▴ 10
0
votes
4
replies
394
views
Extract LRT results for each comparison
LRT DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
votes
7
replies
1.5k
views
LRT test followed by filtering based on LFC
deseq2 LFC LRT
written 5.3 years ago by • 0
1
vote
11
replies
4.3k
views
Time-series Analysis using DESeq2 and LRT test
deseq2 LRT timecourse
updated 2.2 years ago by 42k • written 7.3 years ago by ★ 1.5k
2
votes
2
replies
4.0k
views
understanding edgeR glmLRT
edger lrt
updated 4.4 years ago by 50k • written 4.4 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 5.5 years ago by • 0 • written 7.0 years ago by ▴ 50
5
votes
2
replies
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 6.7 years ago by • 0
1
vote
1
reply
1.2k
views
DESeq2: Is it necessary to include all terms and interactions in LRT tests?
deseq2 lrt
updated 6.7 years ago by ▴ 680 • written 6.7 years ago by • 0
0
votes
4
replies
1.1k
views
Design for DESeq2
LRT deseq2 multiple factor design
6.6 years ago sally_b86 • 0
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
6.3 years ago A ▴ 40
0
votes
3
replies
1.3k
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
1
vote
2
replies
904
views
Interpretation of results names after LRT
DESeq2 LRT multiple time points
updated 6.2 years ago by 42k • written 6.2 years ago by ▴ 40
0
votes
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 6.2 years ago by ▴ 30
4
votes
7
replies
7.7k
views
DESeq2: likelihood ratio test interpretation, multifactor
likelihood ratio test deseq2 LRT
updated 19 months ago by 42k • written 5.8 years ago by ▴ 10
2
votes
4
replies
1.2k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
5.7 years ago Maithê Barros ▴ 10
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 42k • written 5.6 years ago by • 0
1
vote
4
replies
917
views
model for LRT
deseq2 LRT
updated 5.4 years ago by 42k • written 5.4 years ago by • 0
0
votes
4
replies
1.2k
views
DESeq2 Ribosome Profiling Time-series: Significantly Different Results for Wald and LRT test
deseq2 ribosome profiling wald lrt
updated 5.4 years ago by 42k • written 5.4 years ago by ▴ 20
3
votes
3
replies
841
views
clarification of time-series analysis
deseq2 baseline LRT
updated 5.2 years ago by 42k • written 5.2 years ago by ★ 1.5k
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 5.2 years ago by 42k • written 5.2 years ago by • 0
1
vote
1
reply
1.9k
views
DESeq2 test LRT or WALD
deseq2 LRT WALD
updated 4.8 years ago by 42k • written 4.8 years ago by • 0
4
votes
2
replies
9.2k
views
DESeq2 LRT output help
deseq2 LRT anova
9.0 years ago rclaire ▴ 20
1
vote
1
reply
713
views
multifactor desing with interaction LRT or Wald test?
deseq2 LRT wald
updated 4.2 years ago by ★ 3.9k • written 4.2 years ago by ▴ 10
0
votes
8
replies
2.6k
views
DESeq LRT reduced model
deseq2 LRT
updated 4.2 years ago by 42k • written 4.2 years ago by • 0
1
vote
2
replies
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 3.9 years ago by 42k • written 3.9 years ago by • 0
0
votes
1
reply
666
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
updated 3.8 years ago by 42k • written 3.8 years ago by ▴ 30
1
vote
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
votes
1
reply
1.7k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
0
votes
1
reply
561
views
DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2 LRT continuous coeficients
updated 15 months ago by 42k • written 15 months ago by ▴ 10
0
votes
2
replies
774
views
Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2 adjp Volcano LRT
written 18 months ago by ▴ 10
0
votes
1
reply
564
views
DESeq2 LRT not returning genes
LRT linearmodels DESeq2
updated 22 months ago by 42k • written 22 months ago by ▴ 30
0
votes
2
replies
990
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 4.3 years ago by 42k • written 4.3 years ago by • 0
1
vote
5
replies
1.5k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 5.4 years ago by 42k • written 5.4 years ago by • 0
0
votes
3
replies
631
views
Error using DESeq2's nbinomLRT
deseq2 LRT
updated 3.7 years ago by 42k • written 3.7 years ago by ▴ 20
8
votes
2
replies
6.0k
views
interpreting LRT results DESeq2
deseq2 LRT RNA-Seq
updated 9.1 years ago by 42k • written 9.1 years ago by ▴ 90
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 42k • written 7.9 years ago by ▴ 20
2
votes
1
reply
1.3k
views
LRT test with or without betaPrior
deseq2 LRT betaprior
updated 7.7 years ago by 42k • written 7.7 years ago by ▴ 20
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
0
votes
6
replies
2.9k
views
DESeq extract result of lrt for a subset of the samples
deseq2 rnaseq lrt
updated 7.0 years ago by 42k • written 7.0 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 15 months ago by • 0 • written 2.3 years ago by • 0
0
votes
1
reply
817
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
votes
1
reply
689
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2 LRT multifactorial up/down-reg log2FC
updated 17 months ago by 65k • written 17 months ago by ▴ 10
0
votes
3
replies
965
views
Interpretation of LRT results
DESeq2 LRT Heatmap
updated 7 months ago by 65k • written 18 months ago by ▴ 10
0
votes
1
reply
722
views
LRT test in DESeq2 decide on the level of comparisons
DESeq2 LRT Model
updated 2.2 years ago by 42k • written 2.2 years ago by • 0
0
votes
3
replies
912
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
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
49 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
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Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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