Showing : edger • reset
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
updated 4 hours ago by 66k • written 5 hours ago by ▴ 10
2
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3
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154
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 5 days ago by 50k • written 6 days ago by • 0
1
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2
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209
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Citation for edgeR user guide
edgeR
written 27 days ago by ▴ 30
1
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3
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264
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 days ago by 50k • written 7 days ago by • 0
5
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3
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323
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Log-cpm values from limma
limma edgeR RNASeq
updated 11 days ago by 50k • written 4 weeks ago by • 0
4
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2
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643
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
18 days ago • updated 15 days ago gene_bioconductor ▴ 10
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181
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 18 days ago by 50k • written 18 days ago by • 0
4
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6
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479
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FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 29 days ago Jonathan ▴ 10
3
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3
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371
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permutation test in edgeR
rna-seq edgeR
updated 4 weeks ago by 50k • written 6 weeks ago by • 0
6
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10
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1.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 4 weeks ago by • 0 • written 15 months ago by ▴ 10
0
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3
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219
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
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2
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153
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
4 weeks ago prity6459 • 0
9
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12
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7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 4 weeks ago by • 0 • written 8.9 years ago by ▴ 30
1
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3
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371
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
5
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6
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464
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.1k • written 6 weeks ago by ▴ 30
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3
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285
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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
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2
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201
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
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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
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5
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1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 7 weeks ago by 50k • written 11.5 years ago by ▴ 30
3
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5
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417
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
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2
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1.1k
views
library size and fold changes
edgeR edgeR
updated 7 weeks ago by 50k • written 12.5 years ago by ▴ 670
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6
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378
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
5
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3
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748
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 8 weeks ago by ▴ 50
0
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1
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256
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
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
2
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2
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278
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between lane normalization upper quantile
EDASeq edgeR
9 weeks ago elesofi • 0
0
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2
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306
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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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291
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
1
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3
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446
views
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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532
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 11 weeks ago by ▴ 50
0
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11
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801
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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
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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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1
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291
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ExactTest vs QLFTest
edgeR
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
2
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5
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1.4k
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
1
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6
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530
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Library size normalization in methylation count analysis
edgeR MethylationArray
12 weeks ago mico • 0
5
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4
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435
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Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
0
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8
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692
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago Marianna ▴ 20
2
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6
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446
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago tsl0026 • 0
3
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2
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509
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How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
1
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2
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355
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
0
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4
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369
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
2
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3
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394
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
3
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4
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8.7k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.9 years ago by ▴ 30
1
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8
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584
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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
4
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4
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463
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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
0
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5
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647
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Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
6
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7
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615
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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
0
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0
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271
views
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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654
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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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390
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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
50 results • Page 1 of 1
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Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
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After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
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how to control age and gender effect in expression data using DESeq2
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