Showing : edgeR • reset
2
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116
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
2 days ago • updated 1 day ago mohammedtoufiq91 ▴ 10
2
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3
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170
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 8 days ago by 50k • written 8 days ago by • 0
1
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3
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278
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 9 days ago by 50k • written 10 days ago by • 0
0
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1
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183
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 21 days ago by 50k • written 21 days ago by • 0
4
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2
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649
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
21 days ago • updated 17 days ago gene_bioconductor ▴ 10
1
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2
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221
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Citation for edgeR user guide
edgeR
written 4 weeks ago by ▴ 30
4
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6
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488
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FilterByExpr low counts with small sample size
edgeR
5 weeks ago • updated 4 weeks ago Jonathan ▴ 10
0
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2
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158
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
4 weeks ago prity6459 • 0
0
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3
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225
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
5
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3
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327
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Log-cpm values from limma
limma edgeR RNASeq
updated 13 days ago by 50k • written 5 weeks ago by • 0
3
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3
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372
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permutation test in edgeR
rna-seq edgeR
updated 4 weeks ago by 50k • written 6 weeks ago by • 0
1
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3
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373
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
5
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6
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466
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.2k • written 6 weeks ago by ▴ 40
1
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3
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286
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 6 weeks ago by 66k • written 6 weeks ago by • 0
0
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2
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201
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 weeks ago Marianna ▴ 20
0
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4
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450
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
7 weeks ago Lucy ▴ 60
3
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5
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421
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
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6
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379
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
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1
reply
261
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
5
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3
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758
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 8 weeks ago by 50k • written 9 weeks ago by ▴ 50
2
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3
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317
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
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2
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308
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
2
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2
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279
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between lane normalization upper quantile
EDASeq edgeR
10 weeks ago • updated 9 weeks ago elesofi • 0
2
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2
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294
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 weeks ago Sabiha ▴ 20
1
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3
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448
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
3
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4
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549
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 11 weeks ago by 50k • written 11 weeks ago by ▴ 50
0
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1
reply
244
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Different results from DGE using different subgroups in model.matrix
edgeR
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
0
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11
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811
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 11 weeks ago by 50k • written 12 weeks ago by • 0
0
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1
reply
299
views
ExactTest vs QLFTest
edgeR
updated 11 weeks ago by 50k • written 12 weeks ago by • 0
1
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6
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537
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Library size normalization in methylation count analysis
edgeR MethylationArray
12 weeks ago mico • 0
2
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6
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449
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago tsl0026 • 0
5
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4
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441
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Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago pl23 • 0
0
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8
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693
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago Marianna ▴ 20
3
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2
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517
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How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
0
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4
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374
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Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
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2
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357
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
2
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3
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398
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
4
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4
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466
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edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 66k • written 4 months ago by • 0
6
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7
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621
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readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
1
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8
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595
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
0
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0
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275
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
4 months ago Jawahar • 0
2
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4
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665
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
0
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3
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401
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EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
3
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3
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742
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
4
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9
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1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago Luca • 0
0
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1
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328
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download problem
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
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5
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652
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Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
1
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2
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503
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago Sabiha ▴ 20
5
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2
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613
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
1
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2
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474
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
50 results • Page 1 of 1
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Comment: Volcano plot of scRNA-seq data not "centered" by Michael Love 42k
Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…
Answer: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by ATpoint ★ 4.2k
I was talking about the command line version.
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
I tried reading in the .csv version of the SAF with header = F and I'm still getting an error. I'm running: ``` counts <- featureCounts( …
Comment: Using the plotting functions of clusterProfiler / enrichplot with enrichment res by jovel_juan ▴ 30
enrichPlot requirements are rather low. All what it needs is to provide few columns named specifically. I student of mine wrote the first v…
Votes
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
Error when converting Seurat to SingleCellExperiment
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