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5
votes
1
answer
129
views
1
answer
t-statistic from various limma-approaches does not follow the theoretical distribution
limma voom robust regression voomwithqualityweights t-statistic written 22 days ago by brynedal • 30
0
votes
1
answer
105
views
1
answer
Controlling numerical covariates: differential gene expression with limma voom
rnaseq limma R voom differential gene expression written 16 days ago by Onyi Ukay • 0 • updated 16 days ago by mikhael.manurung • 10
2
votes
1
answer
111
views
1
answer
Inconsistent result between limma/voom and DESeq2
rnaseq limma deseq2 voom limma-voom written 20 days ago by bharata1803 • 30 • updated 20 days ago by Gordon Smyth ♦ 35k
3
votes
1
answer
71
views
1
answer
Limma Voom duplicateCorrelation Design
limma duplicatecorrelation voom written 23 days ago by bruce.moran • 20 • updated 22 days ago by Aaron Lun • 21k
2
votes
1
answer
64
views
1
answer
voom variance modeling: lowess curve fitting notation misunderstanding?
voom written 24 days ago by njbernstein • 0 • updated 24 days ago by Gordon Smyth ♦ 35k
5
votes
1
answer
196
views
1
answer
Voom transformation from counts and normalization to negative values
rnaseq limma statistics voom tcga written 12 weeks ago by Beginner • 50 • updated 12 weeks ago by Ryan C. Thompson ♦ 7.1k
1
vote
1
answer
153
views
1
answer
How to extract gene clusters (genes of similar pattern over time) once spline curves are fitted?
limma voom spline time course experiment gene cluster written 6 months ago by h.valipour.k • 0 • updated 6 months ago by Gordon Smyth ♦ 35k
1
vote
1
answer
213
views
1
answer
Error message with Voom with blocked design matrix
limma voom blocked design written 7 months ago by raf4 • 20 • updated 7 months ago by Gordon Smyth ♦ 35k
2
votes
1
answer
232
views
1
answer
Error in ebayes in limma when analyzing GTEx data
limma voom gtex written 8 months ago by Darklings • 0
2
votes
1
answer
207
views
1
answer
Normalize for changes in one direction
rnaseq limma voom written 10 months ago by Jake • 60 • updated 10 months ago by Aaron Lun • 21k
2
votes
1
answer
252
views
1
answer
Minimum in Voomplot
limma voom written 10 months ago by raf4 • 20 • updated 10 months ago by Ryan C. Thompson ♦ 7.1k
0
votes
1
answer
459
views
1
answer
voomWithQualityWeights, design and weights
voom rna-seq limma-voom voomwithqualityweights written 10 months ago by anne.biton • 0 • updated 10 months ago by Matthew Ritchie • 730
2
votes
3
answers
284
views
3
answers
voom command broken in limma_3.34.5?
limma voom written 11 months ago by sjk314 • 0 • updated 11 months ago by Gordon Smyth ♦ 35k
2
votes
1
answer
669
views
1
answer
Limma voom RNA-seq analysis with both categorical and continuous confounders
limma voom written 11 months ago by prathap1708 • 0 • updated 11 months ago by Gordon Smyth ♦ 35k
0
votes
2
answers
299
views
2
answers
Subsetting an EList Object doesn't subset $sample.weights
limma voom elist written 12 months ago by Steve Pederson • 140 • updated 12 months ago by Gordon Smyth ♦ 35k
4
votes
1
answer
333
views
1
answer
Improve limma-voom trend fit to noisy data
limma voom written 12 months ago by jma1991 • 30 • updated 12 months ago by Aaron Lun • 21k
0
votes
2
answers
353
views
2
answers
Clarification regarding analysis with multi-factorial design
limma sva voom multiple factor design written 12 months ago by scanchi • 0
2
votes
1
answer
496
views
1
answer
block design to test two factors with limma
limma voom written 12 months ago by jfertaj • 20 • updated 12 months ago by Aaron Lun • 21k
3
votes
2
answers
475
views
2
answers
Paired Test - Design Matrix and Contrast Matrix Voom and Limma
limma voom paired samples written 12 months ago by rfbrhm • 0 • updated 12 months ago by Gordon Smyth ♦ 35k
4
votes
2
answers
324
views
2
answers
voomWithQualityWeights: question on min. number of replicates per group + design to use
limma edger voom limma-voom voomwithqualityweights written 13 months ago by Guido Hooiveld • 2.3k • updated 12 months ago by Gordon Smyth ♦ 35k
0
votes
0
answers
275
views
0
answers
interGeneCorrelation and voom
limma voom intergenecorrelation written 13 months ago by maltethodberg • 100
10
votes
1
answer
451
views
1
answer
Is there are better way to improve the design via blocking or contrasts while using limma-voom for the mentioned datasets?
limma voom rna-seq limma-voom written 13 months ago by vd4mmind • 0 • updated 13 months ago by Aaron Lun • 21k
0
votes
1
answer
209
views
1
answer
Non-used samples changing number of significant genes in limma
limma voom written 14 months ago by Jake • 60
10
votes
1
answer
2.2k
views
5 follow
1
answer
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq limma edger deseq2 voom written 3.5 years ago by Sean Davis ♦ 21k • updated 15 months ago by Paul Harrison • 60
1
vote
2
answers
390
views
2
answers
Expression profile from $E from Voom
voom $elist written 15 months ago by anpham • 0 • updated 15 months ago by Steve Lianoglou ♦ 12k
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