Showing : VOOM • reset
0
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2
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160
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
15 days ago • updated 14 days ago Gimena • 0
5
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2
replies
505
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
7
votes
2
replies
715
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limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
3
votes
4
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510
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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
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579
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
5
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3
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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 50k • written 6 months ago by ▴ 180
1
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6
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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 ▴ 10
1
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1
reply
932
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 9 months ago by 50k • written 9 months ago by • 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 50k • written 9 months ago by • 0
0
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1
reply
439
views
How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 9 months ago by 65k • written 9 months ago by • 0
0
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1
reply
582
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 12 months ago by 50k • written 12 months ago by • 0
3
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4
replies
1.0k
views
Processing data with voom "expression values" and "weights"
limma voom
updated 15 months ago by 50k • written 15 months ago by • 0
1
vote
1
reply
554
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 15 months ago by 50k • written 15 months ago by • 0
0
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3
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914
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 16 months ago by 50k • written 16 months ago by • 0
1
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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 50k • written 17 months ago by • 0
1
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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 50k • written 21 months ago by ▴ 10
5
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6
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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
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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 50k • written 23 months ago by ▴ 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 50k • written 24 months ago by ▴ 20
0
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3
replies
1.2k
views
limma voom contrasts
contrasts limma voom
updated 2.1 years ago by 50k • written 2.1 years ago by ▴ 90
0
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3
replies
980
views
Need help with a contrast design for limma with a missing group?
limma VOOM
updated 2.1 years ago by 50k • written 2.2 years ago by ▴ 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
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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
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2
replies
1.3k
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 2.6 years ago by 50k • written 2.6 years ago by • 0
0
votes
1
reply
1.8k
views
limma/voom for protein intensity data
limma proteomics voom
updated 2.6 years ago by ★ 4.0k • written 2.6 years ago by ▴ 70
0
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2
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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
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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 50k • written 3.3 years ago by ▴ 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 50k • written 3.6 years ago by ▴ 60
0
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5
replies
1.3k
views
isoform data, deep sequencing and voom
isoform deep sequencing voom
updated 3.7 years ago by 50k • written 3.7 years ago by ▴ 620
0
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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 50k • written 3.8 years ago by ▴ 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 65k • written 3.8 years ago by ▴ 10
0
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1
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787
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 3.8 years ago by 50k • written 3.8 years ago by • 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 50k • written 3.9 years ago by ▴ 10
1
vote
5
replies
1.4k
views
Limma for proteomic data! Please Help!
limma voom lmfit ebayesfit
updated 4.0 years ago by 50k • written 4.0 years ago by • 0
0
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2
replies
644
views
estimating variability in absence of replicates for edgeR
edgeR RNAseq voom variability estimator
updated 4.1 years ago by 50k • written 4.1 years ago by • 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 50k • written 4.1 years ago by • 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 50k • written 4.1 years ago by ▴ 10
0
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0
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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 50k • written 4.3 years ago by ▴ 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 50k • written 4.4 years ago by ▴ 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 50k • written 4.5 years ago by • 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 65k • written 4.5 years ago by ▴ 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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