Showing : edgeR • reset
2
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3
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119
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 3 days ago by 50k • written 3 days ago by • 0
1
vote
2
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204
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Citation for edgeR user guide
edgeR
written 25 days ago by ▴ 30
1
vote
3
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240
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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
5
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3
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307
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Log-cpm values from limma
limma edgeR RNASeq
updated 8 days ago by 50k • written 4 weeks ago by • 0
4
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2
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624
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
16 days ago • updated 12 days ago gene_bioconductor ▴ 10
0
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1
reply
176
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 16 days ago by 50k • written 16 days ago by • 0
4
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6
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469
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FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 26 days ago Jonathan ▴ 10
3
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3
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368
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permutation test in edgeR
rna-seq edgeR
updated 27 days ago by 50k • written 5 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 29 days ago by • 0 • written 15 months ago by ▴ 10
0
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3
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212
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 29 days ago by 50k • written 4 weeks ago by • 0
0
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2
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147
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
29 days ago prity6459 • 0
9
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12
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7.9k
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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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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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459
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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
1
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3
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280
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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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197
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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
0
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5
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1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 6 weeks ago by 50k • written 11.5 years ago by ▴ 30
3
votes
5
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413
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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
0
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6
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372
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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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737
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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
votes
1
reply
252
views
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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310
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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
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
0
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2
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305
views
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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289
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
1
vote
3
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439
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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509
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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11
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793
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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
0
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1
reply
242
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Different results from DGE using different subgroups in model.matrix
edgeR
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
0
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1
reply
287
views
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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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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430
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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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682
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago • updated 12 weeks ago Marianna ▴ 20
2
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6
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442
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago • updated 12 weeks ago tsl0026 • 0
3
votes
2
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500
views
How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
1
vote
2
replies
351
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
0
votes
4
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366
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
2
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3
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386
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • 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
vote
8
replies
579
views
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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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
0
votes
5
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643
views
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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605
views
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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267
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
2
votes
4
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649
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
0
votes
3
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380
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
3
votes
3
replies
717
views
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
50 results • Page 1 of 1
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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