Showing : edger • reset
2
votes
4
replies
1.5k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 3 days ago by 51k • written 7 days ago by • 0
1
vote
8
replies
911
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 10 days ago by • 0
0
votes
1
reply
410
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 13 days ago by 67k • written 13 days ago by • 0
3
votes
3
replies
798
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 19 days ago by • 0
0
votes
4
replies
527
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
20 days ago • updated 17 days ago Philippine • 0
4
votes
6
replies
1.0k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
27 days ago • updated 18 days ago altintas.ali • 0
1
vote
2
replies
275
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
28 days ago Hongjian • 0
3
votes
3
replies
263
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
4 weeks ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
281
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 5 weeks ago by 51k • written 5 weeks ago by • 0
1
vote
1
reply
221
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 6 weeks ago by ★ 4.5k • written 6 weeks ago by • 0
1
vote
2
replies
422
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 6 weeks ago by 42k • written 7 weeks ago by ▴ 10
0
votes
2
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315
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 6 weeks ago by 51k • written 7 weeks ago by • 0
1
vote
2
replies
291
views
Inconsistent result in edgeR
edgeR
8 weeks ago hiroko.ohmiya • 0
1
vote
1
reply
407
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 9 weeks ago by 51k • written 10 weeks ago by • 0
2
votes
9
replies
769
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 11 weeks ago by 51k • written 11 weeks ago by • 0
0
votes
3
replies
467
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 3 months ago by • 0
1
vote
1
reply
564
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 3 months ago by ★ 28k • written 3 months ago by • 0
0
votes
1
reply
341
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 3 months ago by 51k • written 3 months ago by • 0
3
votes
3
replies
526
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 3 months ago by 67k • written 3 months ago by ▴ 50
0
votes
4
replies
543
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 4 months ago by • 0
1
vote
8
replies
902
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 4 months ago by 51k • written 4 months ago by • 0
3
votes
5
replies
1.5k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 4 months ago by • 0 • written 8 months ago by ▴ 50
0
votes
4
replies
569
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
5 months ago vohara4 • 0
3
votes
6
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800
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
5 months ago JG13 • 0
3
votes
2
replies
612
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
5 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
661
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 6 months ago by 51k • written 6 months ago by • 0
1
vote
3
replies
602
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 months ago by 51k • written 6 months ago by • 0
0
votes
1
reply
370
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 6 months ago by 51k • written 6 months ago by • 0
4
votes
2
replies
1.1k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
6 months ago gene_bioconductor ▴ 10
1
vote
2
replies
678
views
Citation for edgeR user guide
edgeR
written 6 months ago by ▴ 30
4
votes
6
replies
955
views
FilterByExpr low counts with small sample size
edgeR
7 months ago • updated 6 months ago Jonathan ▴ 10
0
votes
2
replies
365
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
6 months ago prity6459 • 0
0
votes
3
replies
534
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 6 months ago by 51k • written 7 months ago by • 0
5
votes
3
replies
807
views
Log-cpm values from limma
limma edgeR RNASeq
updated 6 months ago by 51k • written 7 months ago by • 0
3
votes
3
replies
830
views
permutation test in edgeR
rna-seq edgeR
updated 6 months ago by 51k • written 7 months ago by • 0
1
vote
3
replies
618
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 7 months ago by 51k • written 7 months ago by • 0
5
votes
6
replies
842
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 7 months ago by ★ 4.5k • written 7 months ago by ▴ 70
1
vote
3
replies
536
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
0
votes
2
replies
501
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 months ago Marianna ▴ 20
0
votes
4
replies
811
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
7 months ago Lucy ▴ 60
3
votes
5
replies
1.1k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 7 months ago by 51k • written 7 months ago by • 0
0
votes
6
replies
688
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 7 months ago by 51k • written 7 months ago by • 0
0
votes
1
reply
546
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 7 months ago by 51k • written 7 months ago by • 0
6
votes
5
replies
1.6k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 15 days ago by 51k • written 7 months ago by ▴ 50
2
votes
3
replies
559
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 8 months ago by 51k • written 8 months ago by • 0
0
votes
2
replies
554
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 months ago by 51k • written 8 months ago by • 0
2
votes
2
replies
526
views
between lane normalization upper quantile
EDASeq edgeR
8 months ago elesofi • 0
2
votes
2
replies
497
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 months ago Sabiha ▴ 20
1
vote
3
replies
701
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 9 months ago by • 0
0
votes
1
reply
397
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 8 months ago by 51k • written 8 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Comment: Merge Replicates vs Mixed Model by abadgerw • 0
@gabrielhoffman any insight?
Comment: makeContrastsDream for Interaction by abadgerw • 0
@gabrielhoffman any insight?
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta by Michael Love 42k
That is the rows that did converge.
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
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