Showing : EdgeR • reset
4
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2
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544
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
5 days ago • updated 1 day ago gene_bioconductor ▴ 10
0
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1
reply
123
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 5 days ago by 50k • written 5 days ago by • 0
1
vote
1
reply
179
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Citation for edgeR user guide
edgeR
updated 14 days ago by 50k • written 14 days ago by ▴ 30
0
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2
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138
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
18 days ago prity6459 • 0
0
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3
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193
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 18 days ago by 50k • written 19 days ago by • 0
3
votes
1
reply
179
views
Log-cpm values from limma
limma edgeR RNASeq
updated 18 days ago by 50k • written 19 days ago by • 0
4
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6
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438
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FilterByExpr low counts with small sample size
edgeR
20 days ago • updated 15 days ago Jonathan ▴ 10
1
vote
3
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352
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 22 days ago by 50k • written 27 days ago by • 0
5
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6
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433
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 24 days ago by ★ 4.1k • written 28 days ago by ▴ 30
3
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3
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340
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permutation test in edgeR
rna-seq edgeR
updated 16 days ago by 50k • written 29 days ago by • 0
1
vote
3
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265
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
0
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2
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174
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
4 weeks ago Marianna ▴ 20
0
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4
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433
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
5 weeks ago Lucy ▴ 60
3
votes
5
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390
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
6
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359
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
1
reply
236
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
5
votes
3
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715
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 50
2
votes
3
replies
297
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
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2
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285
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
2
votes
2
replies
257
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between lane normalization upper quantile
EDASeq edgeR
7 weeks ago elesofi • 0
2
votes
2
replies
266
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
3
votes
4
replies
435
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 8 weeks ago by 50k • written 9 weeks ago by ▴ 50
0
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1
reply
223
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
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1
reply
258
views
ExactTest vs QLFTest
edgeR
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
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11
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743
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 9 weeks ago by 50k • written 10 weeks ago by • 0
1
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6
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496
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Library size normalization in methylation count analysis
edgeR MethylationArray
10 weeks ago mico • 0
5
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4
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402
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Confusion about LFC using contrasts weights in EdgeR
edgeR
11 weeks ago • updated 10 weeks ago pl23 • 0
2
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6
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419
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
11 weeks ago tsl0026 • 0
0
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8
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643
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
12 weeks ago • updated 11 weeks ago Marianna ▴ 20
3
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2
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446
views
How does one test for interactions in EdgeR?
edgeR
12 weeks ago pl23 • 0
0
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4
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354
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Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
vote
2
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328
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago • updated 12 weeks ago mico • 0
2
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3
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372
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
1
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3
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412
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
6
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7
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574
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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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551
views
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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247
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
2
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4
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599
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
0
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3
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347
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
3
votes
3
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684
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
4
votes
4
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436
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 3 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 • updated 3 months ago Luca • 0
0
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1
reply
313
views
download problem
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
5
replies
623
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
1
vote
2
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470
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
votes
2
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563
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
vote
2
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427
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
7
votes
2
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812
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
0
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3
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460
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
4
votes
2
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640
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DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(fit2, vector_group, probe_annotation, contrasts = contrast_matrix, gs.annots = gs.…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by Gordon Smyth 50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
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