Showing : Timecourse • reset
18
votes
24
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14k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 3.2 years ago by • 0 • written 9.1 years ago by ▴ 120
9
votes
7
replies
9.3k
views
DESeq2 timecourse - How to set the experimental design
deseq2 geneexpression timecourse
updated 9.6 years ago by ★ 13k • written 9.6 years ago by ▴ 10
7
votes
5
replies
1.6k
views
Which is the best design matrix to compare a timecourse between two conditions?
limma voom design matrix timecourse
updated 7.2 years ago by 50k • written 7.2 years ago by ▴ 10
7
votes
9
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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
6
votes
19
replies
3.6k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 6.6 years ago by ▴ 680 • written 6.6 years ago by ▴ 50
6
votes
5
replies
2.2k
views
Limma : design and contrast for a timecourse experiment with 2 cell lines
limma limma design matrix timecourse
8.4 years ago Pierre-François Roux • 0
5
votes
2
replies
1.8k
views
DESeq2 design matrix for timecourse
deseq2 experimental design timecourse rnaseq model
updated 7.5 years ago by 41k • written 7.5 years ago by ▴ 20
5
votes
9
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1.6k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 2.8 years ago by 65k • written 2.8 years ago by ▴ 830
4
votes
6
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2.6k
views
Timecourse Differential expression with multiple factors
deseq2 edger timecourse
7.2 years ago • updated 7.1 years ago anna_stavrinides ▴ 20
4
votes
18
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24k
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DEseq2 time-series design.
deseq2 timecourse design
updated 4.8 years ago by • 0 • written 9.5 years ago by ▴ 100
4
votes
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
4
votes
7
replies
2.6k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 6.5 years ago by 41k • written 7.3 years ago by ▴ 10
4
votes
8
replies
2.2k
views
edgeR: How to set model for glmQLFTest in time-course experiment (compared to glmLRT?
edgeR edger "glmqlftest()" timecourse model
updated 6.7 years ago by ★ 7.9k • written 6.7 years ago by ▴ 10
3
votes
2
replies
977
views
time-series analysis using EdgeR
timecourse edgeR
updated 23 months ago by 50k • written 23 months ago by • 0
3
votes
4
replies
2.7k
views
Bioconductor vignette on Time course experiments only describes how to plot the the gene with the smallest p-value. How can I plot specific genes of …
timecourse time course rna-seq deseq2 ggplot2
8.6 years ago moldach ▴ 20
3
votes
3
replies
1.9k
views
DESeq2 time series: error while measuring gene dispersion.
deseq2 timecourse
updated 9.3 years ago by 41k • written 9.3 years ago by ▴ 40
3
votes
5
replies
1.3k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 9 months ago by 41k • written 10 months ago by • 0
3
votes
7
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2.9k
views
deseq2 complex time course data with out replicates
deseq2 timecourse rnaseq
updated 6.8 years ago by ▴ 680 • written 6.8 years ago by • 0
2
votes
2
replies
1.2k
views
another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 5.9 years ago by 50k • written 5.9 years ago by • 0
2
votes
4
replies
1.3k
views
Standard error of log2FC from DESeq in time series experiment
deseq2 log2fc standard error timecourse
updated 6.2 years ago by • 0 • written 6.2 years ago by • 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
2
votes
3
replies
856
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 4.1 years ago by ★ 3.9k • written 4.1 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
2
votes
1
reply
1.0k
views
DEseq2 time-series before and after Infection
multiple factor design deseq2 timecourse
updated 6.8 years ago by 41k • written 6.8 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
2
votes
0
replies
984
views
List of genes by rank from Timecourse package.
timecourse
9.6 years ago bcur001 ▴ 20
2
votes
3
replies
1.7k
views
Deseq2 time series question,
rnaseq deseq2 timecourse
updated 7.5 years ago by 41k • written 7.5 years ago by • 0
2
votes
3
replies
1.9k
views
What's the criteria used by DESeq2 to calculate log2 fold changes in time-course experiments?
deseq2 timecourse
updated 22 months ago by • 0 • written 6.5 years ago by • 0
2
votes
2
replies
1.2k
views
rlog transformation for Time-course data
deseq2 rlog transformation timecourse rnaseq
updated 7.5 years ago by 41k • written 7.5 years ago by • 0
2
votes
4
replies
4.4k
views
LIMMA on matched time series data
timecourse limma
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 40
2
votes
3
replies
3.3k
views
Analysis of RNA-seq time series with edgeR
edger rna-seq differential expression timecourse time course
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
1
vote
6
replies
911
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
1
vote
1
reply
2.5k
views
DESeq2 time course analysis
DESeq2 Timecourse
updated 3.3 years ago by 41k • written 3.3 years ago by • 0
1
vote
1
reply
1.2k
views
Time Series Analysis
timecourse deseq2
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 20
1
vote
4
replies
2.2k
views
How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 6.2 years ago by 50k • written 6.2 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
1
reply
812
views
DESeq2 timecourse experiments
deseq2 timecourse
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
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
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
1
vote
6
replies
2.7k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.5 years ago by ▴ 10
1
vote
6
replies
1.4k
views
edgeR time series DMSO correction
edger makecontrasts timecourse
updated 7.5 years ago by ★ 7.9k • written 7.5 years ago by ▴ 90
1
vote
3
replies
3.0k
views
DESeq2 analysis for RNAseq data at different time points and different conditions
deseq2 timecourse rnaseq
updated 12 months ago by • 0 • written 7.4 years ago by ▴ 30
1
vote
1
reply
1.3k
views
expression profiles between DESeq2 and Mfuzz
deseq2 mfuzz differential expression timecourse
updated 7.6 years ago by 41k • written 7.6 years ago by ★ 1.5k
1
vote
1
reply
3.0k
views
DESeq2 time series
deseq2 timecourse
updated 7.9 years ago by 41k • written 7.9 years ago by • 0
1
vote
4
replies
2.2k
views
DEXSeq continous variable in model
RNASeq TimeCourse timecourse DEXSeq DESeq2 RNASeq TimeCourse timecourse DEXSeq DESeq2
updated 9.8 years ago by ★ 1.9k • written 9.8 years ago by ▴ 650
1
vote
1
reply
5.5k
views
Mfuzz: fill.NA - Warning messages: argument is not numeric or logical: returning NA
mfuzz clustering bioinformatics proteomics timecourse
updated 8.2 years ago by 1.6k • written 8.2 years ago by • 0
0
votes
0
replies
892
views
Timecourse experiment: wrong experimental design?
TimeCourse probe limma timecourse TimeCourse probe limma timecourse
12.8 years ago Andrea Grilli ▴ 240
0
votes
0
replies
1.0k
views
Bioconductor Digest, Vol 100, Issue 28
GO TimeCourse genefilter timecourse ABarray preprocessCore GeneSelector GO TimeCourse
12.9 years ago Dennis.Burian@faa.gov ▴ 90
0
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0
replies
696
views
timecourse pkg question
TimeCourse convert timecourse TimeCourse convert timecourse
18.0 years ago aaron.j.mackey@gsk.com ▴ 70
0
votes
0
replies
869
views
timecourse: modt1 not found
TimeCourse limma timecourse TimeCourse limma timecourse
13.4 years ago Steve Ladunga ▴ 10
50 results • Page 1 of 1
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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…
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…
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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