Showing : EdgeR • reset
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 1 day ago by 50k • written 1 day ago by • 0
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165
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 21 hours ago by 50k • written 1 day ago by ▴ 10
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1
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165
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Citation for edgeR user guide
edgeR
updated 10 days ago by 50k • written 10 days ago by ▴ 30
4
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6
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414
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FilterByExpr low counts with small sample size
edgeR
16 days ago • updated 11 days ago Jonathan ▴ 10
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2
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127
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
14 days ago prity6459 • 0
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3
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181
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 14 days ago by 50k • written 15 days ago by • 0
3
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1
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165
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Log-cpm values from limma
limma edgeR RNASeq
updated 14 days ago by 50k • written 15 days ago by • 0
3
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3
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326
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permutation test in edgeR
rna-seq edgeR
updated 12 days ago by 50k • written 25 days ago by • 0
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3
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345
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 18 days ago by 50k • written 23 days ago by • 0
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6
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420
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 20 days ago by ★ 4.1k • written 24 days ago by ▴ 30
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3
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244
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 28 days ago by 65k • written 28 days ago by • 0
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165
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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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417
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
4 weeks ago Lucy ▴ 60
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5
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374
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
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6
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352
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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
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1
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233
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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
5
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3
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709
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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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3
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292
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
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2
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281
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
2
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2
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256
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between lane normalization upper quantile
EDASeq edgeR
7 weeks ago • updated 6 weeks ago elesofi • 0
2
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2
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259
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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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402
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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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422
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by ▴ 50
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220
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Different results from DGE using different subgroups in model.matrix
edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
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11
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736
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
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1
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251
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ExactTest vs QLFTest
edgeR
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
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6
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485
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Library size normalization in methylation count analysis
edgeR MethylationArray
9 weeks ago mico • 0
2
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6
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408
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
11 weeks ago • updated 10 weeks ago tsl0026 • 0
5
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4
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389
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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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630
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
11 weeks ago • updated 10 weeks ago Marianna ▴ 20
3
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2
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423
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How does one test for interactions in EdgeR?
edgeR
12 weeks ago • updated 11 weeks ago pl23 • 0
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4
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346
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Nested paired design
edgeR
12 weeks ago manduchi ▴ 10
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2
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324
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
12 weeks ago mico • 0
2
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3
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365
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
4
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4
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431
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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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7
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565
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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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8
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543
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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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244
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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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583
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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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3
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340
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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
3
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3
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670
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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
4
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9
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1.1k
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RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
3 months ago Luca • 0
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1
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309
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download problem
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
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5
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612
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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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2
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461
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
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2
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552
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 5 months ago by • 0
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2
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415
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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
7
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2
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801
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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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3
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454
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
4
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2
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627
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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
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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