Showing : edgeR • reset
10
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13
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1.6k
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edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 1 day ago by 52k • written 3 days ago by ▴ 20
0
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2
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468
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Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
updated 12 days ago by 52k • written 17 days ago by ▴ 10
2
votes
2
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1.2k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 4 weeks ago by ★ 4.8k • written 4 weeks ago by • 0
5
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3
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836
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 5 weeks ago by 52k • written 5 weeks ago by ▴ 10
2
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2
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1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
6 weeks ago • updated 5 weeks ago Elizabeth • 0
0
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2
replies
464
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 5 weeks ago by 43k • written 6 weeks ago by ▴ 20
0
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1
reply
273
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 7 weeks ago by 52k • written 7 weeks ago by • 0
0
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4
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1.1k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 7 weeks ago by • 0 • written 8 weeks ago by • 0
2
votes
4
replies
644
views
EdgeR Biological CVs
edgeR
written 3 months ago by • 0
3
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5
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1.4k
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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
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409
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
3 months ago gingergeiger22 • 0
0
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1
reply
445
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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 3 months ago by 43k • written 4 months ago by • 0
1
vote
8
replies
1.1k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
3 months ago Andre • 0
1
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9
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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 4 months ago by ▴ 10
7
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6
replies
1.1k
views
ANOVA like approach of edgeR
edgeR
updated 4 months ago by 52k • written 5 months ago by ▴ 10
3
votes
3
replies
693
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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
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4
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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
666
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 5 months ago by 68k • written 5 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
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811
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
6 months ago • updated 5 months ago Philippine • 0
4
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6
replies
1.4k
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
474
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
6 months ago Hongjian • 0
3
votes
3
replies
479
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
6 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
494
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 6 months ago by ★ 4.8k • written 6 months ago by • 0
1
vote
2
replies
653
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 6 months ago by 43k • written 7 months ago by ▴ 10
0
votes
2
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561
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 6 months ago by 52k • written 7 months ago by • 0
1
vote
2
replies
495
views
Inconsistent result in edgeR
edgeR
7 months ago hiroko.ohmiya • 0
1
vote
1
reply
642
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 7 months ago by 52k • written 8 months ago by • 0
0
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3
replies
776
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 8 months ago by • 0
1
vote
1
reply
1.5k
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
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1
reply
523
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
767
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
803
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 9 months ago by • 0
1
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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
2.6k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 months ago by • 0 • written 13 months ago by ▴ 60
0
votes
4
replies
822
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
10 months ago vohara4 • 0
3
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6
replies
1.0k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
10 months ago JG13 • 0
3
votes
2
replies
896
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
960
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
839
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
491
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 11 months ago by 52k • written 11 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
11 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
519
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
12 months ago prity6459 • 0
0
votes
3
replies
764
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: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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