Showing : EdgeR • reset
10
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13
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1.7k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 8 days ago by 52k • written 10 days ago by ▴ 20
0
votes
2
replies
484
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
updated 18 days ago by 52k • written 23 days ago by ▴ 10
2
votes
2
replies
1.2k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 5 weeks ago by ★ 4.8k • written 5 weeks ago by • 0
5
votes
3
replies
853
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 6 weeks ago by 52k • written 6 weeks ago by ▴ 10
2
votes
2
replies
1.2k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
7 weeks ago • updated 6 weeks ago Elizabeth • 0
0
votes
2
replies
477
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 6 weeks ago by 43k • written 7 weeks ago by ▴ 20
0
votes
1
reply
277
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 8 weeks ago by 52k • written 8 weeks ago by • 0
0
votes
4
replies
1.2k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 8 weeks ago by • 0 • written 8 weeks ago by • 0
2
votes
4
replies
654
views
EdgeR Biological CVs
edgeR
written 3 months ago by • 0
3
votes
5
replies
1.4k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 3 months ago by 68k • written 3 months ago by ▴ 10
0
votes
2
replies
413
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
3 months ago gingergeiger22 • 0
0
votes
1
reply
452
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 3 months ago by 43k • written 4 months ago by • 0
1
vote
8
replies
1.2k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
4 months ago • updated 3 months ago Andre • 0
1
vote
9
replies
1.1k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 4 months ago by ▴ 30
6
votes
10
replies
2.9k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 4 months ago by ★ 4.8k • written 5 months ago by ▴ 10
7
votes
6
replies
1.1k
views
ANOVA like approach of edgeR
edgeR
updated 5 months ago by 52k • written 5 months ago by ▴ 10
3
votes
3
replies
699
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 5 months ago by 52k • written 5 months ago by • 0
2
votes
4
replies
2.0k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 5 months ago by 52k • written 5 months ago by • 0
1
vote
8
replies
1.9k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 5 months ago by • 0
0
votes
1
reply
693
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 6 months ago by 68k • written 6 months ago by • 0
3
votes
3
replies
1.2k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 6 months ago by • 0
0
votes
4
replies
816
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
6 months ago Philippine • 0
4
votes
6
replies
1.5k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
6 months ago altintas.ali • 0
1
vote
2
replies
478
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
6 months ago Hongjian • 0
3
votes
3
replies
487
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
6 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
498
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 6 months ago by 52k • written 6 months ago by • 0
1
vote
1
reply
389
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 7 months ago by ★ 4.8k • written 7 months ago by • 0
1
vote
2
replies
656
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 7 months ago by 43k • written 7 months ago by ▴ 10
0
votes
2
replies
575
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 7 months ago by 52k • written 7 months ago by • 0
1
vote
2
replies
501
views
Inconsistent result in edgeR
edgeR
7 months ago hiroko.ohmiya • 0
1
vote
1
reply
652
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 7 months ago by 52k • written 7 months ago by • 0
2
votes
9
replies
1.1k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 8 months ago by 52k • written 8 months ago by • 0
0
votes
3
replies
778
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 8 months ago by • 0
1
vote
1
reply
1.6k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 8 months ago by ★ 28k • written 8 months ago by • 0
0
votes
1
reply
525
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 8 months ago by 52k • written 8 months ago by • 0
3
votes
3
replies
772
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 8 months ago by 68k • written 8 months ago by ▴ 60
0
votes
4
replies
810
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 9 months ago by • 0
1
vote
8
replies
1.4k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 9 months ago by 52k • written 10 months ago by • 0
3
votes
5
replies
2.7k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 months ago by • 0 • written 14 months ago by ▴ 60
0
votes
4
replies
829
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
10 months ago vohara4 • 0
3
votes
6
replies
1.0k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
11 months ago JG13 • 0
3
votes
2
replies
907
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
11 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
970
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 11 months ago by 52k • written 11 months ago by • 0
1
vote
3
replies
843
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 11 months ago by 52k • written 11 months ago by • 0
0
votes
1
reply
495
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 12 months ago by 52k • written 12 months ago by • 0
4
votes
2
replies
1.5k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
12 months ago gene_bioconductor ▴ 10
1
vote
2
replies
1.2k
views
Citation for edgeR user guide
edgeR
written 12 months ago by ▴ 30
4
votes
6
replies
1.4k
views
FilterByExpr low counts with small sample size
edgeR
12 months ago Jonathan ▴ 10
0
votes
2
replies
522
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
12 months ago prity6459 • 0
0
votes
3
replies
769
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 12 months ago by 52k • written 12 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an by James W. MacDonald 68k
Have you figured out how to do this using tidy grammar? Using non-tidy grammar is quite simple, and perhaps you already know how to do that…
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You show how you modified the container, but not how you are running it, which is the critical part.
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your reply. > Per sample all counts are scaled by the same size factor so I strongly assume that something was parsed here …
Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k
Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…
Votes
Answer: How to combine two DESeq2 objects (dds) for analysis
How to combine two DESeq2 objects (dds) for analysis
How can I correctly use phyloseq with Docker?
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
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