Showing : multiple time points • reset
0
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3
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1.4k
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DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
5.6 years ago cp1015 • 0
1
vote
4
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1.6k
views
Analysis Time course data using DESeq2
deseq2 timecourse multiple time points time-series
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
2
votes
3
replies
1.9k
views
DESeq2 for time series using time as continuous and looking at effect of time on DE
deseq2 timecourse multiple time points mlr michael love
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
0
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1
reply
959
views
DESeq2 design for time series data without "untreated"
deseq2 rnaseq multiple time points
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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1
reply
1.2k
views
ballgown time course design and command confirmation
ballgown stattest multiple time points
7.1 years ago yadongxue • 0
1
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2
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1.2k
views
Interpretation of results names after LRT
DESeq2 LRT multiple time points
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 60
0
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3
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2.2k
views
Interpretation of the log fold change for a time course/factorial design analysis in limma
limma rnaseq multifactorial design multiple time points
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
1
vote
4
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24k
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Adjusting for covariates in paired sample design DESeq2
deseq2 deseq paired samples covariates multiple time points
7.6 years ago imb ▴ 10
2
votes
8
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3.1k
views
Limma for differential expression in a time-course
limma multiple time points time-course differential expression
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
3
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4
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5.9k
views
DESeq2 Time course analysis design - only time points WITHOUT treatments
rna-seq deseq2 multiple time points
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 10
0
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1
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1.5k
views
Analyze time course experiment with multiple samples from multiple animals with DESeq2
deseq2 multiple factor design multifactorial design multiple time points design and contrast matrix
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 30
5
votes
5
replies
2.8k
views
edgeR : How to test differential exon expression on case/control study across all time points when accounting for the within subject variability?
egdeR multiple time points model.matrix differential exon usage model
7.8 years ago heikki.sarin ▴ 10
0
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1
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1.9k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
2
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5
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2.3k
views
DESeq2 time series tissue specific differences over time
deseq2 timecourse multiple time points rnaseq
7.9 years ago • updated 7.8 years ago Nicholas Owen • 0
5
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30
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6.0k
views
DESeq2 model - How to test case/control time course model when taking account within sample variability?
deseq2 multiple time points time course casecontrol model design
updated 6 weeks ago by • 0 • written 7.9 years ago by ▴ 10
0
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1
reply
2.4k
views
DEseq2 design with paired individuals at two timepoints, two groups and two responses
deseq2 multiple factor design multiple time points paired samples
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
votes
2
replies
3.6k
views
Time-course analysis with limma for >3 time points
limma contrast matrix design matrix multiple time points timecourse
updated 4.0 years ago by • 0 • written 7.9 years ago by ▴ 20
8
votes
9
replies
7.6k
views
DESeq2 time series analysis
DESEQ2 timecourse multiple time points time
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
1
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4
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4.3k
views
DESeq2 time-series data of multiple treatments with common time 0
deseq2 multiple time points multiple treatments
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
1
vote
5
replies
1.8k
views
Differential expression (DESeq2) miRNAseq on patient samples
deseq2 multifactorial design multiple time points
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
2
votes
4
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1.8k
views
DESeq for paired samples from different time stamps
deseq2 multiple time points paired samples
8.1 years ago lironyoffe • 0
2
votes
6
replies
2.6k
views
DESeq2 model design with unequal number of time points
deseq2 multiple time points R
updated 8.2 years ago by ★ 7.9k • written 8.2 years ago by • 0
1
vote
6
replies
2.3k
views
DESeq2: relevel contrasts after DESeq() has been called (time-course experiment of Drosophila development)
drosophila melanogaster multiple time points deseq2 results development
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
4
votes
6
replies
1.9k
views
Multi-factorial design for patient-replicates from different time points (Deseq2)
deseq2 rnaseq timecourse multiple time points multifactorial design
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
2
votes
5
replies
2.2k
views
Need help setting up DESeq2 complex model for multi-dose experiment
deseq2 multiple time points dose
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
1
vote
2
replies
1.3k
views
Correct construction of multiple design matrix with limma in an agilent microarray dataset
limma multiple factor design multiple time points microarray design and contrast matrix
updated 8.6 years ago by 68k • written 8.6 years ago by ▴ 80
1
vote
4
replies
2.1k
views
Effect of treatment vs control over time in RNA Seq (edgeR and limma)
edgeR limma voom RNASeq multiple time points
updated 8.9 years ago by ★ 7.9k • written 8.9 years ago by ▴ 20
3
votes
12
replies
3.2k
views
Questions about complex design in limma regarding an agilent microarray dataset with multiple time points and different biological replicates
limma design matrix multiple time points agilent microarrays
updated 9.2 years ago by ★ 28k • written 9.2 years ago by ▴ 80
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Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Geoff • 0
Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…
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Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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