Showing : edgeR • reset
2
votes
3
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210
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 1 day ago by 51k • written 1 day ago by • 0
2
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4
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1.5k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 10 days ago by 51k • written 14 days ago by • 0
1
vote
8
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964
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 17 days ago by • 0
0
votes
1
reply
422
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 20 days ago by 67k • written 20 days ago by • 0
3
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3
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827
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 26 days ago by • 0
0
votes
4
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555
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
27 days ago • updated 24 days ago Philippine • 0
4
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6
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1.0k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
4 weeks ago • updated 25 days ago altintas.ali • 0
1
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2
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288
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
5 weeks ago Hongjian • 0
3
votes
3
replies
278
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 weeks ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
297
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 6 weeks ago by 51k • written 6 weeks ago by • 0
1
vote
1
reply
225
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 7 weeks ago by ★ 4.5k • written 7 weeks ago by • 0
1
vote
2
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433
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 7 weeks ago by 42k • written 8 weeks ago by ▴ 10
0
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2
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333
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 7 weeks ago by 51k • written 8 weeks ago by • 0
1
vote
2
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302
views
Inconsistent result in edgeR
edgeR
9 weeks ago hiroko.ohmiya • 0
1
vote
1
reply
422
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 10 weeks ago by 51k • written 11 weeks ago by • 0
2
votes
9
replies
783
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Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 12 weeks ago by 51k • written 12 weeks ago by • 0
0
votes
3
replies
477
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 3 months ago by • 0
1
vote
1
reply
598
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
355
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
542
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 3 months ago by 67k • written 3 months ago by ▴ 50
0
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4
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553
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 4 months ago by • 0
1
vote
8
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925
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
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1.5k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 5 months ago by • 0 • written 8 months ago by ▴ 50
0
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4
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577
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
5 months ago vohara4 • 0
3
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6
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811
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
5 months ago JG13 • 0
3
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2
replies
622
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
6 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
673
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
615
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
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1
reply
375
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 6 months ago by 51k • written 6 months ago by • 0
4
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2
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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
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700
views
Citation for edgeR user guide
edgeR
written 7 months ago by ▴ 30
4
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6
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972
views
FilterByExpr low counts with small sample size
edgeR
7 months ago Jonathan ▴ 10
0
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2
replies
370
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
7 months ago prity6459 • 0
0
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3
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548
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 7 months ago by 51k • written 7 months ago by • 0
5
votes
3
replies
828
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
849
views
permutation test in edgeR
rna-seq edgeR
updated 7 months ago by 51k • written 7 months ago by • 0
1
vote
3
replies
622
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
848
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
543
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
509
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 months ago Marianna ▴ 20
0
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4
replies
820
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
696
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
560
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 months ago by 51k • written 8 months ago by • 0
6
votes
5
replies
1.7k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 23 days ago by 51k • written 8 months ago by ▴ 50
2
votes
3
replies
570
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
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2
replies
560
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 months ago by 51k • written 8 months ago by • 0
2
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2
replies
534
views
between lane normalization upper quantile
EDASeq edgeR
8 months ago elesofi • 0
2
votes
2
replies
504
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
708
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 9 months ago by • 0
50 results • Page 1 of 1
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Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0
The updated version worked well on my data. Thank you!
Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di by James W. MacDonald 67k
The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…
Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k
Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…
Comment: Identifying potentially associated gene set to drug response using GSVA by Kent • 0
Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification by James W. MacDonald 67k
You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…
Votes
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
A: TopGO: How to retrieve the gene list related to a GO ID ?
A: Error in DESeqDataSet : some values in assay are not integers
A: correcting the batch effects in Limma and SVA
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