Showing : EdgeR • reset
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 23 days ago by 53k • written 28 days ago by • 0
1
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1
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261
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Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 26 days ago by ★ 5.0k • written 29 days ago by • 0
0
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2
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186
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replace cat with message in glmTreat when lfc = 0
edgeR glmTreat
updated 5 weeks ago by 53k • written 6 weeks ago by • 0
0
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4
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370
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voomLmFit fitted log-CPM values
limma edgeR
updated 7 weeks ago by 53k • written 7 weeks ago by ▴ 10
2
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9
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881
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Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
11 weeks ago mohammedtoufiq91 ▴ 10
3
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2
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838
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Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
3 months ago mohammedtoufiq91 ▴ 10
0
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1
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907
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Using offset in edgeR
edgeR
updated 3 months ago by 53k • written 3 months ago by • 0
4
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8
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1.8k
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Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
3 months ago richardallenfriedmanbrooklyn ▴ 30
7
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9
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5.5k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
3 months ago bbao ▴ 10
5
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11
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3.1k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 6 months ago by ▴ 10
2
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4
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2.6k
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Altered (negative or positive) logFC values for same gene from two intitial count matrices, one being a subset of the other
Transcriptomics edgeR DEG
5 months ago Maziya • 0
2
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3
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1.3k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
5 months ago Paulito • 0
0
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2
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842
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edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 5 months ago by ▴ 110 • written 5 months ago by • 0
0
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3
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952
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Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 6 months ago by ▴ 10
10
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13
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2.5k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 6 months ago by 53k • written 6 months ago by ▴ 20
2
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2
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1.5k
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Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
5
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3
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1.1k
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 7 months ago by 53k • written 7 months ago by ▴ 10
2
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2
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1.5k
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Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
7 months ago Elizabeth • 0
0
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2
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715
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 7 months ago by 43k • written 7 months ago by ▴ 20
0
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1
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420
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 7 months ago by 53k • written 7 months ago by • 0
0
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4
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1.4k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 7 months ago by • 0 • written 8 months ago by • 0
2
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4
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877
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EdgeR Biological CVs
edgeR
written 9 months ago by • 0
3
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5
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1.9k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 9 months ago by 68k • written 9 months ago by ▴ 10
0
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2
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654
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
9 months ago gingergeiger22 • 0
0
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1
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581
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Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 9 months ago by 43k • written 10 months ago by • 0
1
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8
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1.6k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
10 months ago • updated 9 months ago Andre • 0
1
vote
9
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1.5k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 10 months ago by ▴ 40
6
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10
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3.3k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 10 months ago by ★ 5.0k • written 11 months ago by ▴ 10
7
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6
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1.4k
views
ANOVA like approach of edgeR
edgeR
updated 11 months ago by 53k • written 11 months ago by ▴ 10
3
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3
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892
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 11 months ago by 53k • written 11 months ago by • 0
2
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4
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2.4k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 11 months ago by 53k • written 11 months ago by • 0
1
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8
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2.4k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 11 months ago by • 0
0
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1
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868
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single cell RNA seq pseudobulk batch correction
edgeR
updated 12 months ago by 68k • written 12 months ago by • 0
3
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3
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1.5k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 12 months ago by • 0
0
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4
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1.0k
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
12 months ago Philippine • 0
4
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6
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1.8k
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Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
12 months ago altintas.ali • 0
1
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2
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688
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
12 months ago Hongjian • 0
3
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3
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717
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
12 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
641
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 12 months ago by 53k • written 12 months ago by • 0
1
vote
1
reply
581
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
1
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2
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850
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 13 months ago by 43k • written 13 months ago by ▴ 10
0
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2
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765
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 13 months ago by 53k • written 13 months ago by • 0
1
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2
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670
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Inconsistent result in edgeR
edgeR
13 months ago hiroko.ohmiya • 0
1
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1
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838
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Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 13 months ago by 53k • written 14 months ago by • 0
2
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9
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1.4k
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Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 14 months ago by 53k • written 14 months ago by • 0
0
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3
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996
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 14 months ago by • 0
2
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1
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2.1k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 14 months ago by ★ 29k • written 14 months ago by • 0
0
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1
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742
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edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 14 months ago by 53k • written 14 months ago by • 0
3
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3
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1.0k
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Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 14 months ago by 68k • written 14 months ago by ▴ 60
0
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4
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1.0k
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 15 months ago by • 0
2,031 results • Page 1 of 41
Recent ...
Replies
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Votes
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
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