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Voom
•
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13
votes
21
replies
6.0k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma
voom
hurdle
single cell
8.7 years ago
osa.zuta
▴ 40
10
votes
13
replies
3.6k
views
DE for genes with very low counts using limma.
limma
voom
limma-trend
updated 7.5 years ago by
Gordon Smyth
50k • written 7.5 years ago by
maltethodberg
▴ 180
6
votes
13
replies
5.2k
views
How to use RSEM value to find differentially expressed genes
RSEM
limma
edgeR
voom
normalization
updated 21 months ago by
Gordon Smyth
50k • written 3.7 years ago by
harelarik
▴ 60
1
vote
13
replies
6.0k
views
edgeR vs voom
edger
voom
limma
8.8 years ago
dongamit123
▴ 20
3
votes
12
replies
3.9k
views
Problem about use of TCGA rna-seq rsem gene results for regularized cox regression modeling
tcga
rnaseq
glmnet
voom
deseq2
7.1 years ago
panagiotis.mokos
▴ 40
1
vote
12
replies
3.7k
views
Limma-voom design for multifactorial RNA-seq experiment
limma voom
multiple factor design
limma
voom
8.4 years ago
oliver.selmoni
• 0
3
votes
11
replies
2.1k
views
Limma Voom and quadratic regression
limma
voom
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
assaf www
▴ 140
24
votes
11
replies
18k
views
when to apply quantile normalization with voom in limma/voom framework with RNA-seq data?
limma voom
limma
voom
rna-seq
quantile normalization
updated 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
lassancejm
▴ 50
4
votes
10
replies
2.6k
views
Effects of continuous variable with adjustment for gender
edger
limma
voom
updated 8.2 years ago by
Gordon Smyth
50k • written 8.2 years ago by
jhj89
▴ 10
3
votes
10
replies
2.8k
views
Limma voom RNA-seq analysis with both categorical and continuous confounders
limma
voom
updated 6.3 years ago by
Gordon Smyth
50k • written 6.3 years ago by
prathap1708
• 0
1
vote
10
replies
2.1k
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma
voom
20 months ago
Hilary
▴ 30
4
votes
10
replies
2.0k
views
Subject: Strange glitch in Voom curve resulting from batch effects
limma
voom
batcheffect
covariate
updated 7.0 years ago by
Gordon Smyth
50k • written 7.0 years ago by
raf4
▴ 20
2
votes
9
replies
2.3k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA
r
RNASeqData
voom
limma
22 months ago
Peipei
• 0
25
votes
9
replies
6.8k
views
voom for spectral counts
limma
voom
proteomics
spectral counts
massspectrometry
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
Ben Neely
▴ 40
9
votes
9
replies
5.2k
views
Voom on TCGA data shifts count distributions towards negative values
voom
TCGA
RNAseq
9.4 years ago
paola.ostano
▴ 10
10
votes
9
replies
1.7k
views
Is there are better way to improve the design via blocking or contrasts while using limma-voom for the mentioned datasets?
limma-voom
voom
limma
rna-seq
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
vd4mmind
• 0
5
votes
9
replies
5.9k
views
Voom: need at least two non-NA values to interpolate
limma voom
voom
rsem
fpkm
7.7 years ago • updated 7.6 years ago
komal.rathi
▴ 120
4
votes
8
replies
3.2k
views
Visualising effects of observation/sample weights in differential expression analysis
limma
voom
sva
edgeR
updated 9.2 years ago by
Matthew Ritchie
▴ 1000 • written 9.2 years ago by
m.fletcher
▴ 20
11
votes
8
replies
8.6k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA
RNA-Seq
DESeq2
voom
removebatcheffect()
updated 7.6 years ago by
Peter Langfelder
★ 3.0k • written 7.6 years ago by
gokce.ouz
▴ 70
8
votes
8
replies
6.7k
views
Voom transformation from counts and normalization to negative values
rnaseq
voom
limma
tcga
statistics
updated 5.6 years ago by
Ryan C. Thompson
★ 7.9k • written 5.6 years ago by
Beginner
▴ 60
4
votes
7
replies
1.5k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma
voom
edaseq
edger
rnaseq
updated 4.4 years ago by
Gordon Smyth
50k • written 4.4 years ago by
Ahdee
▴ 50
3
votes
7
replies
1.3k
views
Weird results (ribosomal proteins / Y-linked genes) in limma/voom
limma
voom
rnaseq
updated 7.6 years ago by
Gordon Smyth
50k • written 7.6 years ago by
blofeld
▴ 10
2
votes
7
replies
3.4k
views
limma+voom question for effect across multiple tissues
limma
voom
updated 9.5 years ago by
Aaron Lun
★ 28k • written 9.5 years ago by
artvandelay
▴ 10
5
votes
7
replies
2.2k
views
limma - blocking or regressing out nuisance variable
limma
voom
RNA-seq
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
biomiha
▴ 20
2
votes
6
replies
2.1k
views
Three way-interaction on voom (limma) data, including a factor with > 2 levels
RNASeq
limma
voom
anova
updated 2.2 years ago by
tcalvo
▴ 90 • written 6.8 years ago by
David R
▴ 90
4
votes
6
replies
2.7k
views
linear mixed models using edgeR+limma
linear mixed model
edger
limma
voom
RNA-seq
updated 4.0 years ago by
Gordon Smyth
50k • written 4.0 years ago by
weichengz
▴ 10
0
votes
6
replies
3.1k
views
How to use RUVseq with voom-limma for differential expression analysis?
ruvseq
limma
voom
updated 7.7 years ago by
davide risso
▴ 950 • written 7.7 years ago by
brainfood
• 0
3
votes
6
replies
2.4k
views
block design to test two factors with limma
limma
voom
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
jfertaj
▴ 30
3
votes
6
replies
3.2k
views
Understanding voom behavior when model matrix is used with/without intercept for a continuous variable
limma
voom
rnaseq
model.matrix
intercept
updated 4.4 years ago by
Gordon Smyth
50k • written 4.4 years ago by
atakanekiz
▴ 30
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
Camila Orellana
▴ 10
3
votes
6
replies
5.5k
views
RNAseq, what to do if you have no replicates in voom-limma
limma
voom
edger
updated 7.7 years ago by
Konika Chawla
▴ 20 • written 8.8 years ago by
Johnny H
▴ 80
3
votes
6
replies
1.1k
views
Paired RNA-seq experiment with 3 factors using duplicateCorrelation
paired samples
multiple factor design
limma
voom
updated 7.5 years ago by
Gordon Smyth
50k • written 7.5 years ago by
aec
▴ 90
3
votes
6
replies
2.2k
views
Controlling numerical covariates: differential gene expression with limma voom
limma
voom
differential gene expression
rnaseq
R
updated 5.4 years ago by
mikhael.manurung
▴ 270 • written 5.4 years ago by
Onyi Ukay
• 0
2
votes
6
replies
3.3k
views
voom/limma contrast for comparing one level against base-line
limma
voom
contrast
updated 9.1 years ago by
Steve Lianoglou
★ 13k • written 9.1 years ago by
Stijn van Dongen
▴ 80
4
votes
6
replies
1.4k
views
Improve limma-voom trend fit to noisy data
limma
voom
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
jma1991
▴ 70
3
votes
6
replies
1.7k
views
paired and unpaired test at the same time with voom limma
limma
voom
rna-seq
paired test
unpaired test
updated 4.1 years ago by
Gordon Smyth
50k • written 4.1 years ago by
dagsbio
• 0
10
votes
6
replies
4.7k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq
deseq2
edger
voom
limma
updated 6.6 years ago by
Paul Harrison
▴ 100 • written 8.9 years ago by
Sean Davis
21k
3
votes
6
replies
3.1k
views
Pool Single-cells: Analysis
deseq2
single cell
limma
voom
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
Radek
▴ 90
5
votes
6
replies
1.7k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM
avereps
voom
limma
RNASeq
21 months ago
Yang Shi
▴ 10
3
votes
5
replies
2.0k
views
PCA of voom weight values
limma
voom
rnaseq
updated 9.1 years ago by
Gordon Smyth
50k • written 9.1 years ago by
Lorena Pantano
▴ 120
3
votes
5
replies
8.5k
views
limma voom accessing normalised counts tables
limma
rnaseq
geneexpression
voom
counts
updated 9.5 years ago by
Steve Lianoglou
★ 13k • written 9.5 years ago by
Peter Crisp
▴ 10
1
vote
5
replies
1.4k
views
Limma for proteomic data! Please Help!
limma
voom
lmfit
ebayesfit
updated 4.1 years ago by
Gordon Smyth
50k • written 4.1 years ago by
sa825
• 0
16
votes
5
replies
7.4k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma
voom
deseq
normalization
ercc
updated 8.5 years ago by
Gordon Smyth
50k • written 8.5 years ago by
komal.rathi
▴ 120
21
votes
5
replies
14k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma
voom
updated 9.0 years ago by
Gordon Smyth
50k • written 10.0 years ago by
John Blischak
▴ 190
1
vote
5
replies
1.3k
views
Limma-voom read count analysis
Differentially methylated CpG's
Limma
Voom
Read Count
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
ioannis.konstantinidis
• 0
1
vote
5
replies
1.3k
views
Time course experiment using limma with voom
limma
voom
RNA Seq
Time-course experiments
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
mahes.muniandy
• 0
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
Gordon Smyth
50k • written 7.2 years ago by
Camila Orellana
▴ 10
0
votes
5
replies
1.2k
views
Clarification regarding analysis with multi-factorial design
limma
multiple factor design
sva
voom
6.4 years ago
scanchi
• 0
4
votes
5
replies
954
views
Defining the design for a complicated multi-level experiment in Limma
limma
RNASeq
R
voom
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
Colari19
▴ 60
8
votes
5
replies
2.5k
views
How to know if I should use voomWithQualityWeights() or not?
limma
RNA-Seq
voom
voomWithQualityWeights
edgeR
updated 4.1 years ago by
Gordon Smyth
50k • written 4.1 years ago by
pedrodcb
▴ 10
50 results • Page
1 of 1
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Replies
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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