Showing : edgeR • reset
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 1 day ago by 50k • written 2 days ago by ▴ 10
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1
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86
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 2 days ago by 50k • written 2 days ago by • 0
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1
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175
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Citation for edgeR user guide
edgeR
updated 11 days ago by 50k • written 11 days ago by ▴ 30
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2
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131
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
15 days ago prity6459 • 0
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3
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185
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 15 days ago by 50k • written 16 days ago by • 0
3
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1
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173
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Log-cpm values from limma
limma edgeR RNASeq
updated 15 days ago by 50k • written 16 days ago by • 0
4
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6
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425
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FilterByExpr low counts with small sample size
edgeR
17 days ago • updated 12 days ago Jonathan ▴ 10
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3
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347
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 19 days ago by 50k • written 24 days ago by • 0
5
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6
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424
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 21 days ago by ★ 4.1k • written 25 days ago by ▴ 30
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3
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330
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permutation test in edgeR
rna-seq edgeR
updated 13 days ago by 50k • written 26 days ago by • 0
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3
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246
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 29 days ago by 65k • written 29 days ago by • 0
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2
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166
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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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420
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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
3
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5
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382
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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
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6
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355
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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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712
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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 7 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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261
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
3
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4
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426
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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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1
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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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1
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251
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ExactTest vs QLFTest
edgeR
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
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11
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738
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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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6
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490
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Library size normalization in methylation count analysis
edgeR MethylationArray
9 weeks ago mico • 0
5
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4
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392
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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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411
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
11 weeks ago • updated 10 weeks ago tsl0026 • 0
0
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8
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636
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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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427
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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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349
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Nested paired design
edgeR
12 weeks ago manduchi ▴ 10
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325
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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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367
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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
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3
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404
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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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566
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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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547
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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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245
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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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4
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585
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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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341
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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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673
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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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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
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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310
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download problem
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
0
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5
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614
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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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463
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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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557
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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
1
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2
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416
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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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804
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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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458
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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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629
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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: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
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 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
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…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
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
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