Showing : voom • reset
4
votes
4
replies
813
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma adjustment voom removeBatchEffect covariates
4 weeks ago sukeshinik5 • 0
1
vote
2
replies
402
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
11 weeks ago Dylan.Sheerin • 0
0
votes
2
replies
291
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 3 months ago by • 0
0
votes
2
replies
315
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
3 months ago Gimena • 0
5
votes
2
replies
756
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 7 months ago by 51k • written 7 months ago by • 0
7
votes
2
replies
1.1k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 7 months ago by 51k • written 7 months ago by • 0
3
votes
4
replies
675
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
8 months ago pl23 • 0
2
votes
4
replies
744
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
8 months ago Tyler Sagendorf ▴ 10
5
votes
3
replies
796
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 9 months ago by 51k • written 9 months ago by ▴ 180
1
vote
6
replies
2.9k
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 7.7 years ago by ▴ 10
1
vote
1
reply
1.2k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 12 months ago by 51k • written 12 months ago by • 0
1
vote
5
replies
1.2k
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 12 months ago by 51k • written 13 months ago by • 0
0
votes
1
reply
540
views
How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 13 months ago by 66k • written 13 months ago by • 0
0
votes
1
reply
707
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 15 months ago by 51k • written 15 months ago by • 0
3
votes
4
replies
1.3k
views
Processing data with voom "expression values" and "weights"
limma voom
updated 18 months ago by 51k • written 18 months ago by • 0
1
vote
1
reply
626
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 19 months ago by 51k • written 19 months ago by • 0
0
votes
3
replies
1.1k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 20 months ago by 51k • written 20 months ago by • 0
1
vote
1
reply
714
views
Voom variance values: Some minor confusion about which variance is fed to lowess when using a design matrix of covariates
voom
updated 20 months ago by 51k • written 20 months ago by • 0
1
vote
10
replies
2.4k
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma voom
23 months ago Hilary ▴ 40
2
votes
2
replies
1.3k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.0 years ago Yang Shi ▴ 10
2
votes
4
replies
1.5k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 2.0 years ago by 51k • written 2.0 years ago by ▴ 10
5
votes
6
replies
1.9k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
2.0 years ago Yang Shi ▴ 10
2
votes
4
replies
1.6k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
2.0 years ago Yang Shi ▴ 10
2
votes
9
replies
2.5k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
2.1 years ago Peipei • 0
2
votes
2
replies
1.7k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 2.2 years ago by 51k • written 2.2 years ago by ▴ 10
2
votes
4
replies
3.2k
views
Limma: How to deal with multiple batch effects and what is going on under the hood
limma voom
updated 2.2 years ago by 51k • written 2.3 years ago by ▴ 20
0
votes
3
replies
1.5k
views
limma voom contrasts
contrasts limma voom
updated 2.4 years ago by 51k • written 2.4 years ago by ▴ 90
0
votes
3
replies
1.1k
views
Need help with a contrast design for limma with a missing group?
limma VOOM
updated 2.4 years ago by 51k • written 2.4 years ago by ▴ 50
3
votes
5
replies
2.7k
views
limma-trend and voom results do not agree
limma limma-trend voom RNASeq
2.7 years ago • updated 2.6 years ago Tyler Sagendorf ▴ 10
3
votes
2
replies
1.6k
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
2.7 years ago altintas.ali • 0
0
votes
2
replies
2.1k
views
Mean-variance trend and identifying significant DE with large amount of biological change in expression in time-series data
voom
2.7 years ago • updated 2.6 years ago hmviit • 0
0
votes
2
replies
1.4k
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 2.8 years ago by 51k • written 2.8 years ago by • 0
0
votes
1
reply
2.1k
views
limma/voom for protein intensity data
limma proteomics voom
updated 2.9 years ago by ★ 4.2k • written 2.9 years ago by ▴ 70
0
votes
2
replies
1.0k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
2.9 years ago James • 0
0
votes
2
replies
945
views
voom-limma workflow for RNAseq samples with very different numbers of counts
voom limma RNASeq
3.3 years ago annadv • 0
0
votes
2
replies
5.9k
views
TPM data in limma/voom
voom limma DifferentialExpression edgeR
3.4 years ago RJM • 0
1
vote
1
reply
1.5k
views
Limma-Voom - Time series experiment with one group (duplicateCorrelation() function)
voom duplicateCorrelation() timeseries limma
updated 3.6 years ago by 51k • written 3.6 years ago by ▴ 10
6
votes
13
replies
5.6k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 2.0 years ago by 51k • written 3.9 years ago by ▴ 60
0
votes
5
replies
1.4k
views
isoform data, deep sequencing and voom
isoform deep sequencing voom
updated 4.0 years ago by 51k • written 4.0 years ago by ▴ 620
0
votes
4
replies
1.2k
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport isoform voom
updated 4.0 years ago by 51k • written 4.0 years ago by ▴ 620
1
vote
4
replies
1.2k
views
How to compare a single RNA-Seq sample with microarray samples?
voom rna-seq microarray
updated 4.1 years ago by 66k • written 4.1 years ago by ▴ 10
0
votes
1
reply
859
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 4.1 years ago by 51k • written 4.1 years ago by • 0
4
votes
6
replies
3.1k
views
linear mixed models using edgeR+limma
linear mixed model edger limma voom RNA-seq
updated 4.2 years ago by 51k • written 4.2 years ago by ▴ 10
1
vote
5
replies
1.6k
views
Limma for proteomic data! Please Help!
limma voom lmfit ebayesfit
updated 4.3 years ago by 51k • written 4.3 years ago by • 0
0
votes
2
replies
716
views
estimating variability in absence of replicates for edgeR
edgeR RNAseq voom variability estimator
updated 4.3 years ago by 51k • written 4.3 years ago by • 0
3
votes
6
replies
1.9k
views
paired and unpaired test at the same time with voom limma
limma voom rna-seq paired test unpaired test
updated 4.3 years ago by 51k • written 4.3 years ago by • 0
8
votes
5
replies
2.8k
views
How to know if I should use voomWithQualityWeights() or not?
limma RNA-Seq voom voomWithQualityWeights edgeR
updated 4.4 years ago by 51k • written 4.4 years ago by ▴ 10
0
votes
0
replies
851
views
RNAseq/miRNAseq normalization for calculating gene correlations, survival analysis, and exploratory graphing
limma edger voom rnaseq mirnaseq
4.5 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 4.6 years ago by 51k • written 4.6 years ago by ▴ 50
3
votes
6
replies
3.5k
views
Understanding voom behavior when model matrix is used with/without intercept for a continuous variable
limma voom rnaseq model.matrix intercept
updated 4.6 years ago by 51k • written 4.6 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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