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voom
•
reset
0
votes
2
replies
150
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 10 days ago by
taur.vil
• 0
0
votes
2
replies
183
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
29 days ago
Gimena
• 0
5
votes
2
replies
549
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
annikagable
• 0
7
votes
2
replies
797
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
3
votes
4
replies
528
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
5 months ago
pl23
• 0
2
votes
4
replies
603
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
5 months ago
Tyler Sagendorf
▴ 10
5
votes
3
replies
699
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom
blocking
limma
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
Gerhard Thallinger
▴ 180
1
vote
1
reply
974
views
How to do GSEA over limma + voom DGE ?
GSEA
voom
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
manuelsokolov
• 0
1
vote
5
replies
1.0k
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 9 months ago by
Gordon Smyth
50k • written 10 months ago by
manuelsokolov
• 0
0
votes
1
reply
454
views
How to do PFS after Voom + Limma DGE ?
RNASeqData
limma
voom
PFS
DGE
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
manuelsokolov
• 0
0
votes
1
reply
607
views
Decidetest results summary different from results written as .csv file
edgeR
voom
decidetests
DEG
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Ankita
• 0
3
votes
4
replies
1.1k
views
Processing data with voom "expression values" and "weights"
limma
voom
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
Edmond
• 0
1
vote
1
reply
570
views
Alternatives to Voom in experiments without replicate
limma
edgeR
Voom
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
Mohammad
• 0
0
votes
3
replies
945
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR
voom
normalization
DifferentialExpression
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
wiscoyogi
• 0
1
vote
1
reply
655
views
Voom variance values: Some minor confusion about which variance is fed to lowess when using a design matrix of covariates
voom
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
Brian
• 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
2
votes
2
replies
1.2k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma
Clustering
voom
RNA-Seq
21 months ago
Yang Shi
▴ 10
2
votes
4
replies
1.3k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
Yang Shi
▴ 10
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
2
votes
4
replies
1.4k
views
Doing normalization when using voom for DEG analysis?
limma
RSEM
voom
Normalization
21 months ago
Yang Shi
▴ 10
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
2
votes
2
replies
1.5k
views
Handling NA values in limma's voom design matrix
limma
voom
design
NAs
updated 23 months ago by
Gordon Smyth
50k • written 23 months ago by
dr
▴ 10
2
votes
4
replies
2.7k
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
0
votes
3
replies
1.3k
views
limma voom contrasts
contrasts
limma
voom
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 years ago by
S T
▴ 90
0
votes
3
replies
1.0k
views
Need help with a contrast design for limma with a missing group?
limma
VOOM
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 years ago by
Ahdee
▴ 50
3
votes
2
replies
1.4k
views
Multi-level design RRBS analysis with voomLmFit
edgeR
voomLmFit
limma
duplicateCorrelation
voom
2.4 years ago
altintas.ali
• 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
0
votes
2
replies
1.8k
views
Mean-variance trend and identifying significant DE with large amount of biological change in expression in time-series data
voom
2.5 years ago • updated 2.4 years ago
hmviit
• 0
0
votes
2
replies
1.3k
views
voom flips the sign relative to log(cpm)
limma
limma-voom
rnaseq
voom
updated 2.6 years ago by
Gordon Smyth
50k • written 2.6 years ago by
taur.vil
• 0
0
votes
1
reply
1.8k
views
limma/voom for protein intensity data
limma
proteomics
voom
updated 2.6 years ago by
ATpoint
★ 4.1k • written 2.6 years ago by
Endre Sebestyén
▴ 70
0
votes
2
replies
967
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
2.7 years ago
James
• 0
0
votes
2
replies
864
views
voom-limma workflow for RNAseq samples with very different numbers of counts
voom
limma
RNASeq
3.1 years ago
annadv
• 0
0
votes
2
replies
5.3k
views
TPM data in limma/voom
voom
limma
DifferentialExpression
edgeR
3.2 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 3.4 years ago by
Gordon Smyth
50k • written 3.4 years ago by
heikki.sarin
▴ 10
6
votes
13
replies
5.1k
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
0
votes
5
replies
1.3k
views
isoform data, deep sequencing and voom
isoform
deep sequencing
voom
updated 3.7 years ago by
Gordon Smyth
50k • written 3.7 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 3.8 years ago by
Gordon Smyth
50k • written 3.8 years ago by
Ina Hoeschele
▴ 620
1
vote
4
replies
1.0k
views
How to compare a single RNA-Seq sample with microarray samples?
voom
rna-seq
microarray
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
Sam
▴ 10
0
votes
1
reply
800
views
Coefficients not estimable voom Lima with multiple numeric covariate
r
limma
design
rnaseq
voom
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 years ago by
Will
• 0
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
1
vote
5
replies
1.4k
views
Limma for proteomic data! Please Help!
limma
voom
lmfit
ebayesfit
updated 4.0 years ago by
Gordon Smyth
50k • written 4.0 years ago by
sa825
• 0
0
votes
2
replies
658
views
estimating variability in absence of replicates for edgeR
edgeR
RNAseq
voom
variability estimator
updated 4.1 years ago by
Gordon Smyth
50k • written 4.1 years ago by
hcnbox
• 0
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
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
0
votes
0
replies
761
views
RNAseq/miRNAseq normalization for calculating gene correlations, survival analysis, and exploratory graphing
limma
edger
voom
rnaseq
mirnaseq
4.2 years ago
atakanekiz
▴ 30
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
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
0
votes
0
replies
827
views
limma-voom group design and its effect on sva
limma
voom
group-design
sva
4.4 years ago
kentfung
▴ 20
2
votes
4
replies
1.3k
views
Limma gives big p-values for large LFC
limma
voom
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
chipolino
• 0
4
votes
5
replies
951
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
50 results • Page
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Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Votes
Bioconductor 3.19 is Released!
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