Showing : EdgeR • reset
0
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DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 2 hours ago by ★ 4.7k • written 1 day ago by • 0
2
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4
replies
464
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EdgeR Biological CVs
edgeR
updated 5 weeks ago by 52k • written 5 weeks ago by • 0
3
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5
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1.1k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 6 weeks ago by 68k • written 6 weeks ago by ▴ 10
0
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2
replies
307
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
7 weeks ago gingergeiger22 • 0
0
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1
reply
388
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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 8 weeks ago by 43k • written 9 weeks ago by • 0
1
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8
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976
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Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
8 weeks ago • updated 7 weeks ago Andre • 0
1
vote
9
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905
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 10 weeks ago by ▴ 30
6
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10
replies
2.7k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 11 weeks ago by ★ 4.7k • written 3 months ago by ▴ 10
7
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6
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1000
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ANOVA like approach of edgeR
edgeR
updated 3 months ago by 52k • written 3 months ago by ▴ 10
3
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3
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619
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 3 months ago by 52k • written 3 months ago by • 0
2
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4
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1.8k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 3 months ago by 52k • written 3 months ago by • 0
1
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8
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1.4k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 3 months ago by • 0
0
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1
reply
559
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 3 months ago by 68k • written 3 months ago by • 0
3
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3
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1.0k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 4 months ago by • 0
0
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4
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713
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
4 months ago Philippine • 0
4
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6
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1.3k
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Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
4 months ago altintas.ali • 0
1
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2
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395
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edgeR 4.2.2 not compiled for Windows
edger edgeR
4 months ago Hongjian • 0
3
votes
3
replies
400
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
4 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
424
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 4 months ago by 52k • written 4 months ago by • 0
1
vote
1
reply
324
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 5 months ago by ★ 4.7k • written 5 months ago by • 0
1
vote
2
replies
573
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 months ago by 43k • written 5 months ago by ▴ 10
0
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2
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478
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 5 months ago by 52k • written 5 months ago by • 0
1
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2
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415
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Inconsistent result in edgeR
edgeR
5 months ago hiroko.ohmiya • 0
1
vote
1
reply
549
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 5 months ago by 52k • written 5 months ago by • 0
2
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9
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964
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Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 6 months ago by 52k • written 6 months ago by • 0
0
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3
replies
654
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 6 months ago by • 0
1
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1
reply
1.1k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 6 months ago by ★ 28k • written 6 months ago by • 0
0
votes
1
reply
457
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 6 months ago by 52k • written 6 months ago by • 0
3
votes
3
replies
672
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Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 6 months ago by 68k • written 6 months ago by ▴ 50
0
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4
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704
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 7 months ago by • 0
1
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8
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1.2k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 7 months ago by 52k • written 8 months ago by • 0
3
votes
5
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2.2k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 8 months ago by • 0 • written 12 months ago by ▴ 60
0
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4
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729
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
8 months ago vohara4 • 0
3
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6
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944
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
8 months ago JG13 • 0
3
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2
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793
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
9 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
852
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 9 months ago by 52k • written 9 months ago by • 0
1
vote
3
replies
753
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 9 months ago by 52k • written 9 months ago by • 0
0
votes
1
reply
452
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 10 months ago by 52k • written 10 months ago by • 0
4
votes
2
replies
1.3k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
10 months ago • updated 9 months ago gene_bioconductor ▴ 10
1
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2
replies
1.0k
views
Citation for edgeR user guide
edgeR
written 10 months ago by ▴ 30
4
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6
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1.2k
views
FilterByExpr low counts with small sample size
edgeR
10 months ago Jonathan ▴ 10
0
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2
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456
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
10 months ago prity6459 • 0
0
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3
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689
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 10 months ago by 52k • written 10 months ago by • 0
5
votes
3
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1.1k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 9 months ago by 52k • written 10 months ago by • 0
3
votes
3
replies
1.2k
views
permutation test in edgeR
rna-seq edgeR
updated 10 months ago by 52k • written 10 months ago by • 0
1
vote
3
replies
726
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 10 months ago by 52k • written 10 months ago by • 0
5
votes
6
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1.0k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 10 months ago by ★ 4.7k • written 10 months ago by ▴ 70
1
vote
3
replies
632
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 10 months ago by 68k • written 10 months ago by • 0
0
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2
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636
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
11 months ago Marianna ▴ 20
0
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4
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1.0k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
11 months ago Lucy ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Answer: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
I strongly recommend to not concern yourself with these sorts of marginal problems because you're entering a realm in which you're entirely…
Comment: Problem using locateVariants() from the VariantAnnotation package by Marco • 0
Ok, I think I found the problem. By looking at the `locateVariants()` source code, I was able to pinpoint that the problems is when trying …
Comment: Conumee for EPIC and EPICv2 copy number by Adam • 0
As described on the [github](https://github.com/hovestadtlab/conumee2) the way to do this is using array_type = c("EPIC", "EPICv2") This i…
Comment: graper 1.22 Build is Broken by shepherl 4.1k
This is not an appropriate place to report this. this is for usage questions. maintainers are notified automatically when it is failing on …
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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