Showing : timecourse • reset
9
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7
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9.2k
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DESeq2 timecourse - How to set the experimental design
deseq2 geneexpression timecourse
updated 9.5 years ago by ★ 13k • written 9.6 years ago by ▴ 10
1
vote
6
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2.6k
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Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.4 years ago by ▴ 10
0
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3
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2.6k
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Inherits(x,"data.frame") error in SamR
Microarray Normalization Preprocessing Bayesian Clustering TimeCourse Cancer affy vsn LPE
18.2 years ago McGee, Monnie ▴ 300
0
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7
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2.7k
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DESEQ ANODEV : A time course study
TimeCourse timecourse DESeq edgeR
updated 9.4 years ago by 50k • written 10.9 years ago by ▴ 20
0
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5
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3.3k
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coefficients meaning in time course analysis with DESeq2
deseq2 timecourse time course design and contrast matrix coefficient of variation
updated 8.5 years ago by 41k • written 8.5 years ago by ★ 1.5k
1
vote
4
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2.2k
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DEXSeq continous variable in model
RNASeq TimeCourse timecourse DEXSeq DESeq2 RNASeq TimeCourse timecourse DEXSeq DESeq2
updated 9.7 years ago by ★ 1.9k • written 9.7 years ago by ▴ 650
4
votes
18
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24k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 4.8 years ago by • 0 • written 9.5 years ago by ▴ 100
7
votes
5
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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
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
0
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2
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1.1k
views
Time course cDNA two color array analysis
TimeCourse limma timecourse maSigPro TimeCourse limma timecourse maSigPro
17.3 years ago Marcelo Laia ▴ 450
0
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3
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1.4k
views
timecourse + factorial + replicates in LIMMA
TimeCourse timecourse TimeCourse timecourse
updated 16.6 years ago by ★ 6.0k • written 16.6 years ago by ▴ 70
0
votes
3
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1.7k
views
Timeseries loop design analysis using Limma or Maanova?
Bayesian Clustering TimeCourse timecourse oligo Bayesian Clustering TimeCourse timecourse
18.2 years ago Pete ▴ 70
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
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
0
votes
2
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835
views
normalization question (conceptual)
Normalization TimeCourse timecourse Normalization TimeCourse timecourse
updated 19.2 years ago by 65k • written 19.2 years ago by ▴ 30
6
votes
5
replies
2.1k
views
Limma : design and contrast for a timecourse experiment with 2 cell lines
limma limma design matrix timecourse
8.3 years ago Pierre-François Roux • 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
3
votes
2
replies
967
views
time-series analysis using EdgeR
timecourse edgeR
updated 23 months ago by 50k • written 23 months ago by • 0
0
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4
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1.5k
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using timecourse package with non-replicated time course
Microarray TimeCourse timecourse Microarray TimeCourse timecourse
updated 12.8 years ago by ▴ 440 • written 12.8 years ago by ▴ 30
0
votes
7
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1.6k
views
data preparation for timecourse
timecourse
updated 9.4 years ago by ★ 1.5k • written 9.4 years ago by • 0
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
0
votes
10
replies
2.0k
views
advice on limma design when analyzing for final outcome in timecourse data
limma timecourse
updated 9.5 years ago by ▴ 20 • written 9.5 years ago by ▴ 220
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 2.7 years ago by 65k • written 2.7 years ago by ▴ 830
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
4
votes
7
replies
2.6k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 6.4 years ago by 41k • written 7.3 years ago by ▴ 10
0
votes
2
replies
1.1k
views
timecourse package - Missing data
TimeCourse timecourse TimeCourse timecourse
updated 14.2 years ago by ▴ 440 • written 14.2 years ago by ▴ 450
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
0
votes
1
reply
971
views
Finding transcription factors controlling hk1 gene In timecourse experiment
Transcription TimeCourse affy timecourse Transcription TimeCourse affy timecourse
updated 15.0 years ago by ▴ 110 • written 15.0 years ago by ▴ 10
0
votes
3
replies
821
views
RNA seq time course design using DESeq2
deseq2 timecourse
updated 3.6 years ago by 41k • written 3.6 years ago by • 0
1
vote
3
replies
2.9k
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
0
votes
10
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1.6k
views
Timecourse package
Microarray TimeCourse timecourse Microarray TimeCourse timecourse
updated 15.2 years ago by ▴ 440 • written 15.2 years ago by ▴ 380
0
votes
2
replies
1.3k
views
edge, timeseries analysis, model specification question
edge timecourse fittimeseries
updated 8.4 years ago by • 0 • written 8.5 years ago by • 0
0
votes
1
reply
4.4k
views
Error in contrast.fit, LIMMA
TimeCourse timecourse TimeCourse timecourse
updated 15.2 years ago by ★ 1.1k • written 15.2 years ago by ▴ 10
0
votes
3
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1.4k
views
[TimeCourse Package] Warnings message
Genetics TimeCourse timecourse Genetics TimeCourse timecourse
updated 18.3 years ago by ▴ 440 • written 18.3 years ago by ▴ 770
1
vote
6
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1.4k
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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
1
reply
1.3k
views
expression profiles between DESeq2 and Mfuzz
deseq2 mfuzz differential expression timecourse
updated 7.5 years ago by 41k • written 7.6 years ago by ★ 1.5k
0
votes
1
reply
735
views
[OT] Help to creating a function to automate the plotProfile function in timecourse
TimeCourse timecourse TimeCourse timecourse
updated 18.5 years ago by ▴ 320 • written 18.5 years ago by ▴ 770
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
0
votes
2
replies
1.1k
views
Why does the order of data being input matter in Timecourse.R
timecourse
updated 9.5 years ago by 65k • written 9.5 years ago by • 0
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
0
votes
1
reply
924
views
Analysing a timecourse/loop experiment without replication with limma
TimeCourse limma limmaGUI timecourse TimeCourse limma limmaGUI timecourse
updated 18.7 years ago by ★ 6.0k • written 18.7 years ago by ▴ 340
1
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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
3
votes
3
replies
1.9k
views
DESeq2 time series: error while measuring gene dispersion.
deseq2 timecourse
updated 9.2 years ago by 41k • written 9.2 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
1
reply
3.0k
views
DESeq2 time series
deseq2 timecourse
updated 7.8 years ago by 41k • written 7.8 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
0
votes
2
replies
1.4k
views
DE genes over time with DESeq2
deseq2 timecourse design and contrast matrix
updated 6 weeks ago by ▴ 10 • written 8.5 years ago by ★ 1.5k
0
votes
1
reply
763
views
hopach package for clustering
Clustering TimeCourse timecourse Clustering TimeCourse timecourse
updated 18.1 years ago by ▴ 780 • written 18.1 years ago by ▴ 250
0
votes
1
reply
2.7k
views
DESeq: computing 95% CI for negative binomial distribution ?
TimeCourse timecourse DESeq TimeCourse timecourse DESeq
updated 11.0 years ago by 41k • written 11.0 years ago by ▴ 50
0
votes
1
reply
1.7k
views
filtering Gene 1.0 ST chips
TimeCourse probe timecourse oligo TimeCourse probe timecourse oligo
updated 11.2 years ago by ▴ 910 • written 11.2 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
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Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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