Showing : lrt • reset
4
votes
18
replies
6.0k
views
DESeq2 - multifactorial design
LRT DESeq2 interaction
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by ▴ 10
1
vote
11
replies
4.3k
views
Time-series Analysis using DESeq2 and LRT test
deseq2 LRT timecourse
updated 2.1 years ago by 41k • written 7.2 years ago by ★ 1.5k
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
6.2 years ago A ▴ 40
0
votes
8
replies
2.6k
views
DESeq LRT reduced model
deseq2 LRT
updated 4.1 years ago by 41k • written 4.1 years ago by • 0
0
votes
8
replies
2.9k
views
Problems with LRT code using DESeq2
deseq2 LRT differential gene expression
8.4 years ago • updated 8.3 years ago newsomew13 • 0
0
votes
7
replies
1.5k
views
LRT test followed by filtering based on LFC
deseq2 LFC LRT
written 5.2 years ago by • 0
1
vote
7
replies
955
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
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 5.4 years ago by • 0 • written 7.0 years ago by ▴ 50
4
votes
7
replies
7.7k
views
DESeq2: likelihood ratio test interpretation, multifactor
likelihood ratio test deseq2 LRT
updated 18 months ago by 41k • written 5.7 years ago by ▴ 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 41k • written 5.6 years ago by • 0
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 41k • written 7.0 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
1
vote
5
replies
1.4k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 5.4 years ago by 41k • written 5.4 years ago by • 0
2
votes
5
replies
5.5k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.3 years ago rclaire ▴ 20
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 6.1 years ago by ▴ 30
0
votes
4
replies
369
views
Extract LRT results for each comparison
LRT DESeq2
updated 7 months ago by ★ 4.1k • written 7 months 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
2
votes
4
replies
1.2k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
5.6 years ago Maithê Barros ▴ 10
1
vote
4
replies
909
views
model for LRT
deseq2 LRT
updated 5.4 years ago by 41k • 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 5.3 years ago by 41k • written 5.3 years ago by ▴ 20
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
3
replies
934
views
Interpretation of LRT results
DESeq2 LRT Heatmap
updated 7 months ago by 65k • written 18 months ago by ▴ 10
0
votes
3
replies
887
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
3
votes
3
replies
834
views
clarification of time-series analysis
deseq2 baseline LRT
updated 5.2 years ago by 41k • written 5.2 years ago by ★ 1.5k
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 41k • written 7.9 years ago by ▴ 20
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
3
replies
621
views
Error using DESeq2's nbinomLRT
deseq2 LRT
updated 3.7 years ago by 41k • written 3.7 years ago by ▴ 20
0
votes
3
replies
1.2k
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
0
votes
2
replies
759
views
Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2 adjp Volcano LRT
written 17 months ago by ▴ 10
0
votes
2
replies
965
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 4.3 years ago by 41k • written 4.3 years ago by • 0
4
votes
2
replies
9.1k
views
DESeq2 LRT output help
deseq2 LRT anova
9.0 years ago rclaire ▴ 20
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 6.6 years ago by • 0
8
votes
2
replies
6.0k
views
interpreting LRT results DESeq2
deseq2 LRT RNA-Seq
updated 9.1 years ago by 41k • written 9.1 years ago by ▴ 90
2
votes
2
replies
3.9k
views
understanding edgeR glmLRT
edger lrt
updated 4.4 years ago by 50k • written 4.4 years ago by • 0
1
vote
2
replies
895
views
Interpretation of results names after LRT
DESeq2 LRT multiple time points
updated 6.2 years ago by 41k • written 6.2 years ago by ▴ 40
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 41k • written 3.9 years ago by • 0
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 41k • written 5.2 years ago by • 0
0
votes
1
reply
793
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
2
votes
1
reply
1.3k
views
LRT test with or without betaPrior
deseq2 LRT betaprior
updated 7.6 years ago by 41k • written 7.6 years ago by ▴ 20
0
votes
1
reply
677
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2 LRT multifactorial up/down-reg log2FC
updated 16 months ago by 65k • written 16 months 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 41k • written 2.7 years ago by • 0
1
vote
1
reply
704
views
multifactor desing with interaction LRT or Wald test?
deseq2 LRT wald
updated 4.1 years ago by ★ 3.9k • written 4.2 years ago by ▴ 10
0
votes
1
reply
659
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
updated 3.7 years ago by 41k • written 3.7 years ago by ▴ 30
1
vote
1
reply
1.2k
views
DESeq2: Is it necessary to include all terms and interactions in LRT tests?
deseq2 lrt
updated 6.6 years ago by ▴ 680 • written 6.6 years ago by • 0
1
vote
1
reply
1.9k
views
DESeq2 test LRT or WALD
deseq2 LRT WALD
updated 4.7 years ago by 41k • written 4.7 years ago by • 0
0
votes
1
reply
552
views
DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2 LRT continuous coeficients
updated 15 months ago by 41k • written 15 months ago by ▴ 10
0
votes
1
reply
550
views
DESeq2 LRT not returning genes
LRT linearmodels DESeq2
updated 21 months ago by 41k • written 22 months ago by ▴ 30
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
1
reply
710
views
LRT test in DESeq2 decide on the level of comparisons
DESeq2 LRT Model
updated 2.1 years ago by 41k • written 2.1 years ago by • 0
49 results • Page 1 of 1
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Replies
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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