Showing : timecourse • reset
9
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7
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9.3k
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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
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
0
votes
3
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2.6k
views
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
views
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
votes
5
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3.3k
views
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
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
4
votes
18
replies
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
replies
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
votes
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
votes
3
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1.4k
views
timecourse + factorial + replicates in LIMMA
TimeCourse timecourse TimeCourse timecourse
updated 16.7 years ago by ★ 6.0k • written 16.7 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
replies
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
replies
842
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
2.2k
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
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
982
views
time-series analysis using EdgeR
timecourse edgeR
updated 23 months ago by 50k • written 23 months ago by • 0
0
votes
4
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1.5k
views
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
replies
1.6k
views
data preparation for timecourse
timecourse
updated 9.5 years ago by ★ 1.5k • written 9.5 years ago by • 0
4
votes
6
replies
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
replies
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
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 6.5 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
980
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
826
views
RNA seq time course design using DESeq2
deseq2 timecourse
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
1
vote
3
replies
3.0k
views
DESeq2 analysis for RNAseq data at different time points and different conditions
deseq2 timecourse rnaseq
updated 13 months ago by • 0 • written 7.4 years ago by ▴ 30
0
votes
10
replies
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 8.5 years ago by • 0 • written 8.5 years ago by • 0
0
votes
1
reply
4.5k
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
replies
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
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
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
0
votes
1
reply
740
views
[OT] Help to creating a function to automate the plotProfile function in timecourse
TimeCourse timecourse TimeCourse timecourse
updated 18.6 years ago by ▴ 320 • written 18.6 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
929
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 9.3 years ago by 41k • written 9.3 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 7.9 years ago by 41k • written 7.9 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 8 weeks ago by ▴ 10 • written 8.5 years ago by ★ 1.5k
0
votes
1
reply
766
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 11.1 years ago by 41k • written 11.1 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
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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