Showing : Voom • reset
1
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2
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298
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
14 days ago • updated 13 days ago Dylan.Sheerin • 0
0
votes
2
replies
200
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 4 weeks ago by • 0
0
votes
2
replies
210
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
7 weeks ago Gimena • 0
5
votes
2
replies
612
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
7
votes
2
replies
890
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
3
votes
4
replies
572
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
651
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
6 months ago Tyler Sagendorf ▴ 10
5
votes
3
replies
726
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 7 months ago by 50k • written 7 months ago by ▴ 180
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 ▴ 10
1
vote
1
reply
1.0k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 10 months ago by 50k • written 10 months ago by • 0
1
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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 10 months ago by 50k • written 10 months ago by • 0
0
votes
1
reply
482
views
How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 11 months ago by 66k • written 11 months ago by • 0
0
votes
1
reply
635
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 13 months ago by 50k • written 13 months ago by • 0
3
votes
4
replies
1.1k
views
Processing data with voom "expression values" and "weights"
limma voom
updated 16 months ago by 50k • written 16 months ago by • 0
1
vote
1
reply
576
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 17 months ago by 50k • written 17 months ago by • 0
0
votes
3
replies
990
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 18 months ago by 50k • written 18 months ago by • 0
1
vote
1
reply
668
views
Voom variance values: Some minor confusion about which variance is fed to lowess when using a design matrix of covariates
voom
updated 18 months ago by 50k • written 18 months ago by • 0
1
vote
10
replies
2.1k
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma voom
21 months ago • updated 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
22 months ago Yang Shi ▴ 10
2
votes
4
replies
1.4k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 22 months ago by 50k • written 22 months ago by ▴ 10
5
votes
6
replies
1.7k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
22 months ago Yang Shi ▴ 10
2
votes
4
replies
1.4k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
22 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
23 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 2.0 years ago by 50k • written 2.0 years ago by ▴ 10
2
votes
4
replies
2.9k
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 50k • written 2.1 years ago by ▴ 20
0
votes
3
replies
1.3k
views
limma voom contrasts
contrasts limma voom
updated 2.2 years ago by 50k • written 2.2 years ago by ▴ 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 50k • written 2.2 years ago by ▴ 50
3
votes
5
replies
2.5k
views
limma-trend and voom results do not agree
limma limma-trend voom RNASeq
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
2.5 years ago altintas.ali • 0
0
votes
2
replies
1.9k
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 2.7 years ago by 50k • written 2.7 years ago by • 0
0
votes
1
reply
1.9k
views
limma/voom for protein intensity data
limma proteomics voom
updated 2.7 years ago by ★ 4.2k • written 2.7 years ago by ▴ 70
0
votes
2
replies
983
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
893
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
5.4k
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 50k • written 3.4 years ago by ▴ 10
6
votes
13
replies
5.3k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 22 months ago by 50k • written 3.7 years ago by ▴ 60
0
votes
5
replies
1.3k
views
isoform data, deep sequencing and voom
isoform deep sequencing voom
updated 3.8 years ago by 50k • written 3.8 years ago by ▴ 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 50k • written 3.9 years ago by ▴ 620
1
vote
4
replies
1.1k
views
How to compare a single RNA-Seq sample with microarray samples?
voom rna-seq microarray
updated 3.9 years ago by 66k • written 3.9 years ago by ▴ 10
0
votes
1
reply
811
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 3.9 years ago by 50k • written 3.9 years ago by • 0
4
votes
6
replies
2.8k
views
linear mixed models using edgeR+limma
linear mixed model edger limma voom RNA-seq
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 10
1
vote
5
replies
1.4k
views
Limma for proteomic data! Please Help!
limma voom lmfit ebayesfit
updated 4.1 years ago by 50k • written 4.1 years ago by • 0
0
votes
2
replies
670
views
estimating variability in absence of replicates for edgeR
edgeR RNAseq voom variability estimator
updated 4.2 years ago by 50k • written 4.2 years ago by • 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 50k • written 4.2 years ago by • 0
8
votes
5
replies
2.6k
views
How to know if I should use voomWithQualityWeights() or not?
limma RNA-Seq voom voomWithQualityWeights edgeR
updated 4.2 years ago by 50k • written 4.2 years ago by ▴ 10
0
votes
0
replies
789
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 4.4 years ago by 50k • written 4.4 years ago by ▴ 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 50k • written 4.5 years ago by ▴ 30
0
votes
0
replies
837
views
limma-voom group design and its effect on sva
limma voom group-design sva
4.5 years ago kentfung ▴ 20
50 results • Page 1 of 1
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Comment: Volcano plot of scRNA-seq data not "centered" by Michael Love 42k
Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…
Answer: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by ATpoint ★ 4.2k
I was talking about the command line version.
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
I tried reading in the .csv version of the SAF with header = F and I'm still getting an error. I'm running: ``` counts <- featureCounts( …
Comment: Using the plotting functions of clusterProfiler / enrichplot with enrichment res by jovel_juan ▴ 30
enrichPlot requirements are rather low. All what it needs is to provide few columns named specifically. I student of mine wrote the first v…
Votes
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
Error when converting Seurat to SingleCellExperiment
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