Showing : edgeR • reset
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When to use edgeR or limma
edgeR limma
updated 1 hour ago by 68k • written 1 day ago by • 0
3
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4
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148
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Question about the filterByExpr function inputs in edgeR
RNASeq filter design edgeR model.matrix
1 day ago • updated 14 hours ago mohammedtoufiq91 ▴ 10
8
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8
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2.8k
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Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
written 7.3 years ago by ▴ 20
0
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3
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248
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How to do differential expresion across time serise with edgeR?
edgeR timecoursedata
updated 11 days ago by 53k • written 12 days ago by ▴ 10
0
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3
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272
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segfault in edgeR glmQLFit
edgeR
updated 23 days ago by 53k • written 26 days ago by • 0
1
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2
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473
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Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 9 weeks ago by ★ 4.0k • written 3 months ago by • 0
0
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1
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248
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 3 months ago by 53k • written 3 months ago by • 0
2
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2
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352
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replace cat with message in glmTreat when lfc = 0
edgeR glmTreat
updated 3 months ago by 53k • written 4 months ago by • 0
0
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4
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475
views
voomLmFit fitted log-CPM values
limma edgeR
updated 4 months ago by 53k • written 4 months ago by ▴ 10
2
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9
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1.0k
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Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
5 months ago mohammedtoufiq91 ▴ 10
3
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2
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985
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Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
5 months ago mohammedtoufiq91 ▴ 10
0
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1
reply
978
views
Using offset in edgeR
edgeR
updated 6 months ago by 53k • written 6 months ago by • 0
4
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8
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2.0k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
6 months ago richardallenfriedmanbrooklyn ▴ 30
7
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9
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5.8k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
5
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11
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3.6k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 8 months ago by ▴ 10
2
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4
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2.7k
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Altered (negative or positive) logFC values for same gene from two intitial count matrices, one being a subset of the other
Transcriptomics edgeR DEG
7 months ago Maziya • 0
2
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3
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1.6k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
7 months ago Paulito • 0
0
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2
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936
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edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 7 months ago by ▴ 110 • written 7 months ago by • 0
0
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3
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1.1k
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Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 9 months ago by ▴ 10
10
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13
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3.0k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 8 months ago by 53k • written 8 months ago by ▴ 20
2
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2
replies
1.6k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
5
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3
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1.3k
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 10 months ago by 53k • written 10 months ago by ▴ 10
2
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2
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1.7k
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Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
10 months ago Elizabeth • 0
0
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2
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817
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 10 months ago by 43k • written 10 months ago by ▴ 20
0
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1
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486
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 10 months ago by 53k • written 10 months ago by • 0
0
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4
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1.5k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 10 months ago by • 0 • written 10 months ago by • 0
2
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4
replies
1.0k
views
EdgeR Biological CVs
edgeR
written 12 months ago by • 0
3
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5
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2.3k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 12 months ago by 68k • written 12 months ago by ▴ 10
0
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2
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782
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
12 months ago gingergeiger22 • 0
0
votes
1
reply
649
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Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
1
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8
replies
1.7k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
12 months ago Andre • 0
1
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9
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1.7k
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 13 months ago by ▴ 40
6
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10
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3.6k
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What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 13 months ago by ★ 5.0k • written 13 months ago by ▴ 10
7
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6
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1.5k
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ANOVA like approach of edgeR
edgeR
updated 13 months ago by 53k • written 13 months ago by ▴ 10
3
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3
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999
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 14 months ago by 53k • written 14 months ago by • 0
2
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4
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2.7k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 14 months ago by 53k • written 14 months ago by • 0
1
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8
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2.7k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 14 months ago by • 0
0
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1
reply
940
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 14 months ago by 68k • written 14 months ago by • 0
3
votes
3
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1.6k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 14 months ago by • 0
0
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4
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1.2k
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
14 months ago Philippine • 0
4
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6
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1.9k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
15 months ago • updated 14 months ago altintas.ali • 0
1
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2
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762
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
15 months ago Hongjian • 0
3
votes
3
replies
821
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
15 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
712
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 15 months ago by 53k • written 15 months ago by • 0
1
vote
1
reply
742
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
1
vote
2
replies
948
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 15 months ago by 43k • written 15 months ago by ▴ 10
0
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2
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859
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 15 months ago by 53k • written 15 months ago by • 0
1
vote
2
replies
737
views
Inconsistent result in edgeR
edgeR
16 months ago hiroko.ohmiya • 0
1
vote
1
reply
918
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 16 months ago by 53k • written 16 months ago by • 0
2
votes
9
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1.6k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 16 months ago by 53k • written 16 months ago by • 0
2,035 results • Page 1 of 41
Recent ...
Replies
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: Quality control of shotgun metagenomics data by James W. MacDonald 68k
This support site is meant primarily for helping people with technical questions about using Bioconductor packages. For general analysis qu…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Votes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
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