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Showing :
Voom
•
reset
1
vote
2
replies
345
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
5 weeks ago
Dylan.Sheerin
• 0
0
votes
2
replies
227
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 7 weeks ago by
taur.vil
• 0
0
votes
2
replies
248
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
10 weeks ago
Gimena
• 0
5
votes
2
replies
672
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 6 months ago by
Gordon Smyth
51k • written 6 months ago by
annikagable
• 0
7
votes
2
replies
989
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 6 months ago by
Gordon Smyth
51k • written 6 months ago by
annikagable
• 0
3
votes
4
replies
599
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
6 months ago
pl23
• 0
2
votes
4
replies
686
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
7 months ago
Tyler Sagendorf
▴ 10
5
votes
3
replies
747
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom
blocking
limma
updated 8 months ago by
Gordon Smyth
51k • written 8 months ago by
Gerhard Thallinger
▴ 180
1
vote
6
replies
2.8k
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 7.6 years ago by
Camila Orellana
▴ 10
1
vote
1
reply
1.1k
views
How to do GSEA over limma + voom DGE ?
GSEA
voom
limma
updated 11 months ago by
Gordon Smyth
51k • written 11 months ago by
manuelsokolov
• 0
1
vote
5
replies
1.1k
views
Does voom normalization quantile create difference in DGE genes when distribution of patients is similar (no big differences in quantiles)?
limmaGUI
normalization
limma
voom
Normalization
updated 11 months ago by
Gordon Smyth
51k • written 11 months ago by
manuelsokolov
• 0
0
votes
1
reply
505
views
How to do PFS after Voom + Limma DGE ?
RNASeqData
limma
voom
PFS
DGE
updated 11 months ago by
James W. MacDonald
66k • written 11 months ago by
manuelsokolov
• 0
0
votes
1
reply
665
views
Decidetest results summary different from results written as .csv file
edgeR
voom
decidetests
DEG
updated 14 months ago by
Gordon Smyth
51k • written 14 months ago by
Ankita
• 0
3
votes
4
replies
1.2k
views
Processing data with voom "expression values" and "weights"
limma
voom
updated 17 months ago by
Gordon Smyth
51k • written 17 months ago by
Edmond
• 0
1
vote
1
reply
591
views
Alternatives to Voom in experiments without replicate
limma
edgeR
Voom
updated 17 months ago by
Gordon Smyth
51k • written 17 months ago by
Mohammad
• 0
0
votes
3
replies
1.0k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR
voom
normalization
DifferentialExpression
updated 18 months ago by
Gordon Smyth
51k • written 18 months ago by
wiscoyogi
• 0
1
vote
1
reply
684
views
Voom variance values: Some minor confusion about which variance is fed to lowess when using a design matrix of covariates
voom
updated 19 months ago by
Gordon Smyth
51k • written 19 months ago by
Brian
• 0
1
vote
10
replies
2.2k
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma
voom
21 months ago
Hilary
▴ 30
2
votes
2
replies
1.3k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma
Clustering
voom
RNA-Seq
23 months ago
Yang Shi
▴ 10
2
votes
4
replies
1.4k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 23 months ago by
Gordon Smyth
51k • written 23 months ago by
Yang Shi
▴ 10
5
votes
6
replies
1.8k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM
avereps
voom
limma
RNASeq
23 months ago
Yang Shi
▴ 10
2
votes
4
replies
1.5k
views
Doing normalization when using voom for DEG analysis?
limma
RSEM
voom
Normalization
23 months ago
Yang Shi
▴ 10
2
votes
9
replies
2.4k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA
r
RNASeqData
voom
limma
24 months ago
Peipei
• 0
2
votes
2
replies
1.6k
views
Handling NA values in limma's voom design matrix
limma
voom
design
NAs
updated 2.1 years ago by
Gordon Smyth
51k • written 2.1 years ago by
dr
▴ 10
2
votes
4
replies
3.0k
views
Limma: How to deal with multiple batch effects and what is going on under the hood
limma
voom
updated 2.1 years ago by
Gordon Smyth
51k • written 2.1 years ago by
jmannhei
▴ 20
0
votes
3
replies
1.4k
views
limma voom contrasts
contrasts
limma
voom
updated 2.3 years ago by
Gordon Smyth
51k • written 2.3 years ago by
S T
▴ 90
0
votes
3
replies
1.1k
views
Need help with a contrast design for limma with a missing group?
limma
VOOM
updated 2.3 years ago by
Gordon Smyth
51k • written 2.3 years ago by
Ahdee
▴ 50
3
votes
5
replies
2.6k
views
limma-trend and voom results do not agree
limma
limma-trend
voom
RNASeq
2.6 years ago • updated 2.5 years ago
Tyler Sagendorf
▴ 10
3
votes
2
replies
1.5k
views
Multi-level design RRBS analysis with voomLmFit
edgeR
voomLmFit
limma
duplicateCorrelation
voom
2.6 years ago
altintas.ali
• 0
0
votes
2
replies
2.0k
views
Mean-variance trend and identifying significant DE with large amount of biological change in expression in time-series data
voom
2.6 years ago • updated 2.5 years ago
hmviit
• 0
0
votes
2
replies
1.4k
views
voom flips the sign relative to log(cpm)
limma
limma-voom
rnaseq
voom
updated 2.7 years ago by
Gordon Smyth
51k • written 2.7 years ago by
taur.vil
• 0
0
votes
1
reply
1.9k
views
limma/voom for protein intensity data
limma
proteomics
voom
updated 2.8 years ago by
ATpoint
★ 4.2k • written 2.8 years ago by
Endre Sebestyén
▴ 70
0
votes
2
replies
999
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
2.8 years ago
James
• 0
0
votes
2
replies
920
views
voom-limma workflow for RNAseq samples with very different numbers of counts
voom
limma
RNASeq
3.2 years ago
annadv
• 0
0
votes
2
replies
5.6k
views
TPM data in limma/voom
voom
limma
DifferentialExpression
edgeR
3.3 years ago
RJM
• 0
1
vote
1
reply
1.4k
views
Limma-Voom - Time series experiment with one group (duplicateCorrelation() function)
voom
duplicateCorrelation()
timeseries
limma
updated 3.5 years ago by
Gordon Smyth
51k • written 3.5 years ago by
heikki.sarin
▴ 10
6
votes
13
replies
5.4k
views
How to use RSEM value to find differentially expressed genes
RSEM
limma
edgeR
voom
normalization
updated 23 months ago by
Gordon Smyth
51k • written 3.8 years ago by
harelarik
▴ 60
0
votes
5
replies
1.3k
views
isoform data, deep sequencing and voom
isoform
deep sequencing
voom
updated 3.9 years ago by
Gordon Smyth
51k • written 3.9 years ago by
Ina Hoeschele
▴ 620
0
votes
4
replies
1.1k
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport
isoform
voom
updated 3.9 years ago by
Gordon Smyth
51k • written 3.9 years ago by
Ina Hoeschele
▴ 620
1
vote
4
replies
1.1k
views
How to compare a single RNA-Seq sample with microarray samples?
voom
rna-seq
microarray
updated 4.0 years ago by
James W. MacDonald
66k • written 4.0 years ago by
Sam
▴ 10
0
votes
1
reply
829
views
Coefficients not estimable voom Lima with multiple numeric covariate
r
limma
design
rnaseq
voom
updated 4.0 years ago by
Gordon Smyth
51k • written 4.0 years ago by
Will
• 0
4
votes
6
replies
2.9k
views
linear mixed models using edgeR+limma
linear mixed model
edger
limma
voom
RNA-seq
updated 4.1 years ago by
Gordon Smyth
51k • written 4.1 years ago by
weichengz
▴ 10
1
vote
5
replies
1.5k
views
Limma for proteomic data! Please Help!
limma
voom
lmfit
ebayesfit
updated 4.2 years ago by
Gordon Smyth
51k • written 4.2 years ago by
sa825
• 0
0
votes
2
replies
682
views
estimating variability in absence of replicates for edgeR
edgeR
RNAseq
voom
variability estimator
updated 4.2 years ago by
Gordon Smyth
51k • written 4.2 years ago by
hcnbox
• 0
3
votes
6
replies
1.8k
views
paired and unpaired test at the same time with voom limma
limma
voom
rna-seq
paired test
unpaired test
updated 4.2 years ago by
Gordon Smyth
51k • written 4.2 years ago by
dagsbio
• 0
8
votes
5
replies
2.7k
views
How to know if I should use voomWithQualityWeights() or not?
limma
RNA-Seq
voom
voomWithQualityWeights
edgeR
updated 4.3 years ago by
Gordon Smyth
51k • written 4.3 years ago by
pedrodcb
▴ 10
0
votes
0
replies
813
views
RNAseq/miRNAseq normalization for calculating gene correlations, survival analysis, and exploratory graphing
limma
edger
voom
rnaseq
mirnaseq
4.3 years ago
atakanekiz
▴ 30
4
votes
7
replies
1.6k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma
voom
edaseq
edger
rnaseq
updated 4.5 years ago by
Gordon Smyth
51k • written 4.5 years ago by
Ahdee
▴ 50
3
votes
6
replies
3.3k
views
Understanding voom behavior when model matrix is used with/without intercept for a continuous variable
limma
voom
rnaseq
model.matrix
intercept
updated 4.5 years ago by
Gordon Smyth
51k • written 4.5 years ago by
atakanekiz
▴ 30
0
votes
0
replies
851
views
limma-voom group design and its effect on sva
limma
voom
group-design
sva
4.5 years ago
kentfung
▴ 20
50 results • Page
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Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
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James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
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Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
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• 0
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