Showing : edgeR • reset
8
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8
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2.8k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
written 7.3 years ago by ▴ 20
0
votes
3
replies
232
views
How to do differential expresion across time serise with edgeR?
edgeR timecoursedata
updated 9 days ago by 53k • written 10 days ago by ▴ 10
0
votes
3
replies
265
views
segfault in edgeR glmQLFit
edgeR
updated 21 days ago by 53k • written 24 days ago by • 0
1
vote
2
replies
471
views
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
votes
1
reply
246
views
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
votes
2
replies
345
views
replace cat with message in glmTreat when lfc = 0
edgeR glmTreat
updated 3 months ago by 53k • written 3 months ago by • 0
0
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4
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474
views
voomLmFit fitted log-CPM values
limma edgeR
updated 4 months ago by 53k • written 4 months ago by ▴ 10
2
votes
9
replies
1.0k
views
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
votes
2
replies
975
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
5 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
975
views
Using offset in edgeR
edgeR
updated 5 months ago by 53k • written 5 months ago by • 0
4
votes
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
votes
9
replies
5.8k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
5
votes
11
replies
3.6k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 8 months ago by ▴ 10
2
votes
4
replies
2.7k
views
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
votes
2
replies
929
views
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
replies
1.1k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 9 months ago by ▴ 10
10
votes
13
replies
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
votes
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
votes
3
replies
1.3k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 9 months ago by 53k • written 10 months ago by ▴ 10
2
votes
2
replies
1.7k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
10 months ago Elizabeth • 0
0
votes
2
replies
814
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 10 months ago by 43k • written 10 months ago by ▴ 20
0
votes
1
reply
484
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
votes
4
replies
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
votes
4
replies
1.0k
views
EdgeR Biological CVs
edgeR
written 11 months ago by • 0
3
votes
5
replies
2.3k
views
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
votes
2
replies
777
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
12 months ago gingergeiger22 • 0
0
votes
1
reply
644
views
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
vote
8
replies
1.7k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
12 months ago Andre • 0
1
vote
9
replies
1.7k
views
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
votes
10
replies
3.6k
views
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
replies
1.5k
views
ANOVA like approach of edgeR
edgeR
updated 13 months ago by 53k • written 13 months ago by ▴ 10
3
votes
3
replies
996
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 13 months ago by 53k • written 13 months ago by • 0
2
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4
replies
2.7k
views
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
vote
8
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2.7k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 14 months ago by • 0
0
votes
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
replies
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
votes
4
replies
1.2k
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
14 months ago Philippine • 0
4
votes
6
replies
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
vote
2
replies
762
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
15 months ago Hongjian • 0
3
votes
3
replies
817
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
15 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
708
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
740
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
946
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 15 months ago by 43k • written 15 months ago by ▴ 10
0
votes
2
replies
857
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
735
views
Inconsistent result in edgeR
edgeR
16 months ago hiroko.ohmiya • 0
1
vote
1
reply
913
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
replies
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
0
votes
3
replies
1.2k
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 17 months ago by • 0
2
votes
1
reply
2.4k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 17 months ago by ★ 29k • written 17 months ago by • 0
2,033 results • Page 1 of 41
Recent ...
Replies
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 10
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Comment: Opportunity to host EuroBioC2026 Preconference workshops! by TikTsokaas33ocissalpc • 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Votes
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
A: Conversion from counts to FPKM
Awards • All
Great Question to fl ▴ 20
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
Popular Question to Hervé Pagès 16k
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