Showing : EdgeR • reset
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 4 days ago by 50k • written 5 days ago by • 0
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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
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Citation for edgeR user guide
edgeR
updated 13 days ago by 50k • written 14 days ago by ▴ 30
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FilterByExpr low counts with small sample size
edgeR
20 days ago • updated 15 days ago Jonathan ▴ 10
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
18 days ago prity6459 • 0
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3
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 18 days ago by 50k • written 19 days ago by • 0
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1
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179
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Log-cpm values from limma
limma edgeR RNASeq
updated 18 days ago by 50k • written 19 days ago by • 0
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339
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permutation test in edgeR
rna-seq edgeR
updated 16 days ago by 50k • written 29 days ago by • 0
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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
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431
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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
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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
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174
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
4 weeks ago Marianna ▴ 20
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4
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431
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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
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5
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
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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
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236
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
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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
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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
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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
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257
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between lane normalization upper quantile
EDASeq edgeR
7 weeks ago elesofi • 0
2
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2
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266
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
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3
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412
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
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4
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435
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 8 weeks ago by 50k • written 9 weeks ago by ▴ 50
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223
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Different results from DGE using different subgroups in model.matrix
edgeR
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
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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
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258
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ExactTest vs QLFTest
edgeR
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
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495
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Library size normalization in methylation count analysis
edgeR MethylationArray
10 weeks ago mico • 0
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418
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
11 weeks ago tsl0026 • 0
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Confusion about LFC using contrasts weights in EdgeR
edgeR
11 weeks ago • updated 10 weeks ago pl23 • 0
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8
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643
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
12 weeks ago • updated 11 weeks ago Marianna ▴ 20
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442
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How does one test for interactions in EdgeR?
edgeR
12 weeks ago pl23 • 0
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354
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Nested paired design
edgeR
3 months ago • updated 12 weeks ago manduchi ▴ 10
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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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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
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436
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edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 3 months ago by • 0
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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
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551
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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
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
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347
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EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
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3
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683
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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
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1.1k
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RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago • updated 3 months ago Luca • 0
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312
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download problem
edgeR
updated 3 months ago by 50k • written 4 months ago by • 0
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5
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622
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Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
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469
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
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2
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562
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
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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
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
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637
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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
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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)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
Votes
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
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
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