Showing : edgeR • reset
2
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3
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124
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 3 days ago by 50k • written 4 days ago by • 0
1
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3
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248
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 4 days ago by 50k • written 5 days ago by • 0
4
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2
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629
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
17 days ago • updated 13 days ago gene_bioconductor ▴ 10
0
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1
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178
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 16 days ago by 50k • written 17 days ago by • 0
1
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2
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204
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Citation for edgeR user guide
edgeR
written 26 days ago by ▴ 30
0
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2
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150
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
4 weeks ago prity6459 • 0
0
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3
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217
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
5
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3
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313
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Log-cpm values from limma
limma edgeR RNASeq
updated 9 days ago by 50k • written 4 weeks ago by • 0
4
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6
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474
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FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 27 days ago Jonathan ▴ 10
1
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3
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369
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
5
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6
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462
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
3
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3
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368
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permutation test in edgeR
rna-seq edgeR
updated 28 days ago by 50k • written 5 weeks ago by • 0
1
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3
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282
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
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2
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198
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
0
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4
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448
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
6 weeks ago Lucy ▴ 60
3
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5
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414
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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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6
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373
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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
0
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1
reply
252
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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
5
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3
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739
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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
2
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3
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313
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
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2
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305
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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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275
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between lane normalization upper quantile
EDASeq edgeR
9 weeks ago • updated 8 weeks ago elesofi • 0
2
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2
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289
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
3
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4
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510
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 50
0
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1
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243
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
0
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1
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288
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ExactTest vs QLFTest
edgeR
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
0
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11
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796
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
1
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6
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528
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Library size normalization in methylation count analysis
edgeR MethylationArray
11 weeks ago mico • 0
5
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4
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431
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Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
2
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6
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444
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago tsl0026 • 0
0
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8
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687
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago • updated 12 weeks ago Marianna ▴ 20
3
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2
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504
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How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
0
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4
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367
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Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
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2
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351
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
2
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3
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388
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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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440
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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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608
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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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582
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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
0
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0
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268
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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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651
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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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384
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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
3
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3
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720
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EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
4
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4
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457
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edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 4 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
4 months ago Luca • 0
0
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1
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326
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download problem
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
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5
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646
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Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
1
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2
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498
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago • updated 4 months ago Sabiha ▴ 20
5
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2
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603
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
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2
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463
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
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2
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864
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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
50 results • Page 1 of 1
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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