Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
Voom
•
reset
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
1
vote
13
replies
6.0k
views
edgeR vs voom
edger
voom
limma
8.8 years ago
dongamit123
▴ 20
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
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
2
votes
3
replies
1.2k
views
voom command broken in limma_3.34.5?
limma
voom
updated 6.3 years ago by
Gordon Smyth
50k • written 6.3 years ago by
sjk314
• 0
3
votes
5
replies
2.5k
views
limma-trend and voom results do not agree
limma
limma-trend
voom
RNASeq
2.5 years ago • updated 2.4 years ago
Tyler Sagendorf
▴ 10
11
votes
3
replies
1.8k
views
Fit a multinomial to RNA-seq count data
voom
limma
glm
multinomial
regression
updated 7.8 years ago by
Robert Castelo
★ 3.3k • written 7.8 years ago by
rubi
▴ 110
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
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
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
4
replies
2.0k
views
Voom nornalization lowess span
voom
normalization
updated 8.1 years ago by
Gordon Smyth
50k • written 8.1 years ago by
Gregory Warnes
▴ 50
2
votes
4
replies
2.8k
views
Limma: How to deal with multiple batch effects and what is going on under the hood
limma
voom
updated 2.0 years ago by
Gordon Smyth
50k • written 2.0 years ago by
jmannhei
▴ 20
1
vote
10
replies
2.1k
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma
voom
20 months ago
Hilary
▴ 30
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
0
votes
4
replies
1.1k
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport
isoform
voom
updated 3.8 years ago by
Gordon Smyth
50k • written 3.8 years ago by
Ina Hoeschele
▴ 620
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
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
5
votes
2
replies
554
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 4 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
10
votes
4
replies
4.4k
views
Filtering lowly expressed genes in voom-limma analysis
voom
limma
rna-seq
differential gene expression
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
rubi
▴ 110
2
votes
2
replies
1.1k
views
Different results from limma depending on whether or not I have an intercept term in my model
limma
lmfit
voom
limma design matrix
voomwithqualityweights
updated 5.4 years ago by
Gordon Smyth
50k • written 5.4 years ago by
kediggins
▴ 10
3
votes
3
replies
3.2k
views
Voom without design matrix
limma
voom
9.3 years ago
Ninni Nahm
▴ 50
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
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
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
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
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
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
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
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
0
votes
2
replies
1.1k
views
Subsetting an EList Object doesn't subset $sample.weights
voom
EList
limma
updated 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
Steve Pederson
▴ 170
7
votes
3
replies
4.3k
views
VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
r
limma
voom
vsn
updated 17 months ago by
Gordon Smyth
50k • written 5.2 years ago by
Sebastian Hesse
▴ 70
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
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
4
votes
4
replies
2.6k
views
Expression profile from $E from Voom
Voom
$EList
updated 6.6 years ago by
Steve Lianoglou
★ 13k • written 6.6 years ago by
anpham
▴ 60
4
votes
3
replies
1.1k
views
Where is the source code for qAbundanceDist?
voom
updated 7.6 years ago by
Gordon Smyth
50k • written 7.6 years ago by
kjo
▴ 70
12
votes
4
replies
4.4k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 5.3 years ago by
Gordon Smyth
50k • written 6.9 years ago by
wd
▴ 30
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
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
8
votes
2
replies
2.5k
views
limma-voom when testing differential expression of a subset of genes.
limma
voom
differential gene expression
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
ankur.chakravarthy.10
▴ 40
3
votes
2
replies
2.2k
views
Paired Test - Design Matrix and Contrast Matrix Voom and Limma
limma
voom
paired samples
updated 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
rfbrhm
• 0
6
votes
4
replies
4.2k
views
RSEM expected counts to limma-voom
limma
voom
rsem
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
Jake
▴ 90
13
votes
2
replies
3.1k
views
voom with combat
limma
voom
combat
batch effect
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
eldronzhou
▴ 10
4
votes
3
replies
2.2k
views
mean-variance corrected data from voom
limma
voom
updated 8.2 years ago by
Gordon Smyth
50k • written 8.2 years ago by
Laure Cougnaud
▴ 20
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
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
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
5
votes
2
replies
1.3k
views
voomWithQualityWeights: question on min. number of replicates per group + design to use
limma
edger
voom
voomWithQualityWeights
limma-voom
updated 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
Guido Hooiveld
★ 3.9k
8
votes
3
replies
2.7k
views
[Limma] Testing continuous variable with interaction
limma
voom
continuous
interactions
confounding
7.6 years ago
lanhuong
▴ 20
4
votes
3
replies
1.7k
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma
voom
variancePartition
dream
updated 4.6 years ago by
gabriel.hoffman
▴ 110 • written 4.8 years ago by
Ben
▴ 50
0
votes
2
replies
1.1k
views
Further analysis of gene expression data
limma
voom
rnaseq
updated 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
bharata1803
▴ 60
50 results • Page
1 of 1
Recent ...
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
Awards
• All
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Zainab
• 0
Popular Question
to
Theo
▴ 10
Popular Question
to
gene_bioconductor
▴ 10
Popular Question
to
rohitsatyam102
▴ 20
Locations
• All
France,
21 minutes ago
Sweden,
32 minutes ago
WEHI, Melbourne, Australia,
1 hour ago
Miami, FL,
2 hours ago
Sweden,
2 hours ago
Traffic: 472 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6