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VOOM
•
reset
0
votes
2
replies
160
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
15 days ago • updated 14 days ago
Gimena
• 0
5
votes
2
replies
505
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
715
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
annikagable
• 0
3
votes
4
replies
510
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
4 months ago
pl23
• 0
2
votes
4
replies
579
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
5 months ago
Tyler Sagendorf
▴ 10
5
votes
3
replies
678
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
6
replies
2.6k
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 7.4 years ago by
Camila Orellana
▴ 10
1
vote
1
reply
932
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
994
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 9 months ago by
manuelsokolov
• 0
0
votes
1
reply
439
views
How to do PFS after Voom + Limma DGE ?
RNASeqData
limma
voom
PFS
DGE
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
manuelsokolov
• 0
0
votes
1
reply
582
views
Decidetest results summary different from results written as .csv file
edgeR
voom
decidetests
DEG
updated 12 months ago by
Gordon Smyth
50k • written 12 months ago by
Ankita
• 0
3
votes
4
replies
1.0k
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
554
views
Alternatives to Voom in experiments without replicate
limma
edgeR
Voom
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
Mohammad
• 0
0
votes
3
replies
914
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR
voom
normalization
DifferentialExpression
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
wiscoyogi
• 0
1
vote
1
reply
637
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
2.0k
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma
voom
20 months ago • updated 19 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
1.3k
views
Doing normalization when using voom for DEG analysis?
limma
RSEM
voom
Normalization
21 months ago
Yang Shi
▴ 10
2
votes
9
replies
2.2k
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
1.4k
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
2.6k
views
Limma: How to deal with multiple batch effects and what is going on under the hood
limma
voom
updated 24 months ago by
Gordon Smyth
50k • written 24 months ago by
jmannhei
▴ 20
0
votes
3
replies
1.2k
views
limma voom contrasts
contrasts
limma
voom
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
S T
▴ 90
0
votes
3
replies
980
views
Need help with a contrast design for limma with a missing group?
limma
VOOM
updated 2.1 years ago by
Gordon Smyth
50k • written 2.2 years ago by
Ahdee
▴ 50
3
votes
5
replies
2.4k
views
limma-trend and voom results do not agree
limma
limma-trend
voom
RNASeq
2.4 years ago
Tyler Sagendorf
▴ 10
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
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
2.4 years ago • updated 2.3 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
★ 4.0k • written 2.6 years ago by
Endre Sebestyén
▴ 70
0
votes
2
replies
951
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
2.6 years ago
James
• 0
0
votes
2
replies
850
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
5.2k
views
TPM data in limma/voom
voom
limma
DifferentialExpression
edgeR
3.2 years ago • updated 3.1 years ago
RJM
• 0
1
vote
1
reply
1.3k
views
Limma-Voom - Time series experiment with one group (duplicateCorrelation() function)
voom
duplicateCorrelation()
timeseries
limma
updated 3.3 years ago by
Gordon Smyth
50k • written 3.3 years ago by
heikki.sarin
▴ 10
6
votes
13
replies
5.0k
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 3.6 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
1.0k
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
999
views
How to compare a single RNA-Seq sample with microarray samples?
voom
rna-seq
microarray
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
Sam
▴ 10
0
votes
1
reply
787
views
Coefficients not estimable voom Lima with multiple numeric covariate
r
limma
design
rnaseq
voom
updated 3.8 years ago by
Gordon Smyth
50k • written 3.8 years ago by
Will
• 0
4
votes
6
replies
2.6k
views
linear mixed models using edgeR+limma
linear mixed model
edger
limma
voom
RNA-seq
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 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
644
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
7
votes
5
replies
2.4k
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
743
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 4.3 years ago by
Gordon Smyth
50k • written 4.3 years ago by
Ahdee
▴ 50
3
votes
6
replies
3.1k
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
816
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
1.2k
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
943
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
1 of 1
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Comment: Error in champ.load(): The following specified files do not exist
by
Basti
▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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