Showing : multiple time points • reset
5
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27
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3.7k
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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 3.4 years ago by 41k • written 6.8 years ago by ▴ 10
3
votes
12
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2.8k
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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 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 80
7
votes
9
replies
7.0k
views
DESeq2 time series analysis
DESEQ2 timecourse multiple time points time
updated 6.9 years ago by 41k • written 6.9 years ago by ▴ 10
2
votes
8
replies
2.5k
views
Limma for differential expression in a time-course
limma multiple time points time-course differential expression
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
1
vote
6
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1.9k
views
DESeq2: relevel contrasts after DESeq() has been called (time-course experiment of Drosophila development)
drosophila melanogaster multiple time points deseq2 results development
updated 7.1 years ago by 41k • written 7.1 years ago by • 0
2
votes
6
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2.1k
views
DESeq2 model design with unequal number of time points
deseq2 multiple time points R
updated 7.1 years ago by ★ 7.9k • written 7.1 years ago by • 0
4
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6
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1.5k
views
Multi-factorial design for patient-replicates from different time points (Deseq2)
deseq2 rnaseq timecourse multiple time points multifactorial design
updated 7.2 years ago by 41k • written 7.2 years ago by • 0
5
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5
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2.3k
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
6.8 years ago • updated 6.7 years ago heikki.sarin ▴ 10
1
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5
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1.5k
views
Differential expression (DESeq2) miRNAseq on patient samples
deseq2 multifactorial design multiple time points
updated 7.0 years ago by 41k • written 7.0 years ago by • 0
2
votes
5
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1.8k
views
Need help setting up DESeq2 complex model for multi-dose experiment
deseq2 multiple time points dose
updated 7.2 years ago by 41k • written 7.2 years ago by • 0
2
votes
5
replies
1.8k
views
DESeq2 time series tissue specific differences over time
deseq2 timecourse multiple time points rnaseq
6.8 years ago Nicholas Owen • 0
3
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4
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5.3k
views
DESeq2 Time course analysis design - only time points WITHOUT treatments
rna-seq deseq2 multiple time points
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 10
2
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4
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1.4k
views
DESeq for paired samples from different time stamps
deseq2 multiple time points paired samples
7.1 years ago lironyoffe • 0
1
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4
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3.7k
views
DESeq2 time-series data of multiple treatments with common time 0
deseq2 multiple time points multiple treatments
updated 7.0 years ago by 41k • written 7.0 years ago by • 0
1
vote
4
replies
1.3k
views
Analysis Time course data using DESeq2
deseq2 timecourse multiple time points time-series
updated 5.8 years ago by 41k • written 5.8 years ago by • 0
1
vote
4
replies
20k
views
Adjusting for covariates in paired sample design DESeq2
deseq2 deseq paired samples covariates multiple time points
6.6 years ago imb ▴ 10
1
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4
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1.7k
views
Effect of treatment vs control over time in RNA Seq (edgeR and limma)
edgeR limma voom RNASeq multiple time points
updated 7.9 years ago by ★ 7.9k • written 7.9 years ago by ▴ 20
0
votes
3
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949
views
DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
4.6 years ago cp1015 • 0
0
votes
3
replies
1.7k
views
Interpretation of the log fold change for a time course/factorial design analysis in limma
limma rnaseq multifactorial design multiple time points
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
2
votes
3
replies
1.5k
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 5.8 years ago by 41k • written 5.9 years ago by • 0
1
vote
2
replies
1.1k
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 7.5 years ago by 65k • written 7.5 years ago by ▴ 80
0
votes
2
replies
3.0k
views
Time-course analysis with limma for >3 time points
limma contrast matrix design matrix multiple time points timecourse
updated 3.0 years ago by • 0 • written 6.8 years ago by ▴ 20
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
0
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1
reply
1.5k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 6.8 years ago by 41k • written 6.8 years ago by • 0
0
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1
reply
1.8k
views
DEseq2 design with paired individuals at two timepoints, two groups and two responses
deseq2 multiple factor design multiple time points paired samples
updated 6.8 years ago by 41k • written 6.8 years ago by • 0
0
votes
1
reply
1.3k
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 6.7 years ago by 41k • written 6.7 years ago by ▴ 30
0
votes
1
reply
903
views
ballgown time course design and command confirmation
ballgown stattest multiple time points
6.1 years ago yadongxue • 0
0
votes
1
reply
725
views
DESeq2 design for time series data without "untreated"
deseq2 rnaseq multiple time points
updated 6.0 years ago by 41k • written 6.0 years ago by • 0
28 results • Page 1 of 1
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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…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM() by James W. MacDonald 65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Votes
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
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Scholar to Rory Stark ★ 5.2k
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