Showing : EdgeR • reset
4
votes
2
replies
207
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When to use edgeR or limma
edgeR limma
updated 5 days ago by 53k • written 7 days ago by • 0
3
votes
4
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242
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Question about the filterByExpr function inputs in edgeR
RNASeq filter design edgeR model.matrix
8 days ago • updated 7 days ago mohammedtoufiq91 ▴ 10
8
votes
8
replies
2.9k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
written 7.4 years ago by ▴ 20
0
votes
3
replies
272
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How to do differential expresion across time serise with edgeR?
edgeR timecoursedata
updated 18 days ago by 53k • written 19 days ago by ▴ 10
0
votes
3
replies
287
views
segfault in edgeR glmQLFit
edgeR
updated 29 days ago by 53k • written 4 weeks ago by • 0
1
vote
2
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478
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Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 10 weeks ago by ★ 4.0k • written 3 months ago by • 0
0
votes
1
reply
250
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 3 months ago by 53k • written 3 months ago by • 0
2
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2
replies
363
views
replace cat with message in glmTreat when lfc = 0
edgeR glmTreat
updated 4 months ago by 53k • written 4 months ago by • 0
0
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4
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482
views
voomLmFit fitted log-CPM values
limma edgeR
updated 4 months ago by 53k • written 4 months ago by ▴ 10
2
votes
9
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1.1k
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
5 months ago mohammedtoufiq91 ▴ 10
3
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2
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1.0k
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
6 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
985
views
Using offset in edgeR
edgeR
updated 6 months ago by 53k • written 6 months ago by • 0
4
votes
8
replies
2.0k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
6 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
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5.8k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
5
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11
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3.7k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 8 months ago by ▴ 10
2
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4
replies
2.7k
views
Altered (negative or positive) logFC values for same gene from two intitial count matrices, one being a subset of the other
Transcriptomics edgeR DEG
8 months ago • updated 7 months ago Maziya • 0
2
votes
3
replies
1.6k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
0
votes
2
replies
942
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edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 8 months ago by ▴ 110 • written 8 months ago by • 0
0
votes
3
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1.1k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 9 months ago by ▴ 10
10
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13
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3.0k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 9 months ago by 53k • written 9 months ago by ▴ 20
2
votes
2
replies
1.6k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
5
votes
3
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1.3k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 10 months ago by 53k • written 10 months ago by ▴ 10
2
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2
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1.7k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
10 months ago Elizabeth • 0
0
votes
2
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829
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 10 months ago by 43k • written 10 months ago by ▴ 20
0
votes
1
reply
489
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 10 months ago by 53k • written 10 months ago by • 0
0
votes
4
replies
1.5k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 10 months ago by • 0 • written 10 months ago by • 0
2
votes
4
replies
1.0k
views
EdgeR Biological CVs
edgeR
written 12 months ago by • 0
3
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5
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2.3k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 12 months ago by 68k • written 12 months ago by ▴ 10
0
votes
2
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795
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
12 months ago gingergeiger22 • 0
0
votes
1
reply
658
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 12 months ago by 43k • written 13 months ago by • 0
1
vote
8
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1.7k
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Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
12 months ago Andre • 0
1
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9
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1.7k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 13 months ago by ▴ 40
6
votes
10
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3.7k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 13 months ago by ★ 5.0k • written 14 months ago by ▴ 10
7
votes
6
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1.5k
views
ANOVA like approach of edgeR
edgeR
updated 14 months ago by 53k • written 14 months ago by ▴ 10
3
votes
3
replies
1.0k
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 14 months ago by 53k • written 14 months ago by • 0
2
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4
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2.7k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 14 months ago by 53k • written 14 months ago by • 0
1
vote
8
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2.7k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 14 months ago by • 0
0
votes
1
reply
943
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 14 months ago by 68k • written 14 months ago by • 0
3
votes
3
replies
1.6k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 15 months ago by • 0
0
votes
4
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1.2k
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
15 months ago Philippine • 0
4
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6
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1.9k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
15 months ago altintas.ali • 0
1
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2
replies
766
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
15 months ago Hongjian • 0
3
votes
3
replies
828
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
15 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
729
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 15 months ago by 53k • written 15 months ago by • 0
1
vote
1
reply
747
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
1
vote
2
replies
956
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 16 months ago by 43k • written 16 months ago by ▴ 10
0
votes
2
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868
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 15 months ago by 53k • written 16 months ago by • 0
1
vote
2
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741
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Inconsistent result in edgeR
edgeR
16 months ago hiroko.ohmiya • 0
1
vote
1
reply
925
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 16 months ago by 53k • written 16 months ago by • 0
2
votes
9
replies
1.7k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 17 months ago by 53k • written 17 months ago by • 0
2,035 results • Page 1 of 41
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Replies
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
I think that some historical context will help here. Aaron Lun was a PhD student in my Lab back in 2015, and the analysis approach that he …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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