Showing : VOOM • reset
0
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124
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 8 days ago by 50k • written 8 days ago by • 0
0
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2
replies
179
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
27 days ago Gimena • 0
5
votes
2
replies
544
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
785
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
526
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
2
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4
replies
596
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
5
votes
3
replies
697
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
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
969
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
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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 50k • written 10 months ago by • 0
0
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1
reply
452
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How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 10 months ago by 65k • written 10 months ago by • 0
0
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1
reply
602
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 12 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 15 months ago by 50k • written 15 months ago by • 0
1
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1
reply
563
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 16 months ago by 50k • written 16 months ago by • 0
0
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3
replies
939
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diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 17 months ago by 50k • written 17 months ago by • 0
1
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1
reply
652
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
vote
10
replies
2.0k
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 50k • written 21 months ago by ▴ 10
5
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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
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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
1.5k
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
2.7k
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 50k • written 2.0 years ago by ▴ 20
0
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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
998
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
2.4k
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
2.5 years ago • updated 2.4 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
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1
reply
1.8k
views
limma/voom for protein intensity data
limma proteomics voom
updated 2.6 years ago by ★ 4.1k • written 2.6 years ago by ▴ 70
0
votes
2
replies
964
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
2.7 years ago James • 0
0
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2
replies
861
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
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1
reply
1.4k
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
5.1k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 21 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 3.7 years ago by 50k • written 3.7 years ago by ▴ 620
0
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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 50k • written 3.8 years ago by ▴ 620
1
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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 65k • written 3.9 years ago by ▴ 10
0
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1
reply
797
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
2.7k
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
votes
2
replies
656
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
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 50k • written 4.1 years ago by ▴ 10
0
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0
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760
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 50k • written 4.4 years ago by ▴ 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 50k • written 4.4 years ago by ▴ 30
0
votes
0
replies
826
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 50k • written 4.5 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Awards • All
Popular Question to junhui.li11 • 0
Scholar to James W. MacDonald 65k
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