Showing : Voom • reset
0
votes
2
replies
155
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 11 days ago by • 0
0
votes
2
replies
187
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
4 weeks ago Gimena • 0
5
votes
2
replies
557
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 5 months ago by • 0
7
votes
2
replies
802
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
531
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
605
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
5
votes
3
replies
704
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
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
982
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
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 10 months ago by 50k • written 10 months ago by • 0
0
votes
1
reply
456
views
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
votes
1
reply
610
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 15 months ago by 50k • written 15 months ago by • 0
1
vote
1
reply
571
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 16 months ago by 50k • written 16 months ago by • 0
0
votes
3
replies
952
views
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
vote
1
reply
658
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
2.1k
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 50k • written 21 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
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 24 months ago by 50k • written 24 months ago by ▴ 10
2
votes
4
replies
2.8k
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
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 • updated 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
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 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 ★ 4.1k • written 2.6 years ago by ▴ 70
0
votes
2
replies
968
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
866
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 50k • written 3.4 years ago by ▴ 10
6
votes
13
replies
5.2k
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
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 50k • written 3.8 years ago by ▴ 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 65k • written 3.9 years ago by ▴ 10
0
votes
1
reply
801
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 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
658
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
votes
0
replies
765
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
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 50k • written 4.5 years ago by • 0
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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