Showing : EDGER • reset
1
vote
6
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186
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
updated 1 hour ago by 52k • written 1 day ago by ▴ 30
6
votes
10
replies
2.4k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 9 days ago by ★ 4.6k • written 21 days ago by ▴ 10
7
votes
6
replies
839
views
ANOVA like approach of edgeR
edgeR
updated 21 days ago by 52k • written 26 days ago by ▴ 10
3
votes
3
replies
528
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 28 days ago by 52k • written 28 days ago by • 0
2
votes
4
replies
1.6k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 5 weeks ago by 52k • written 5 weeks ago by • 0
1
vote
8
replies
1.1k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 6 weeks ago by • 0
0
votes
1
reply
456
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
3
votes
3
replies
888
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 7 weeks ago by • 0
0
votes
4
replies
615
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
7 weeks ago Philippine • 0
4
votes
6
replies
1.1k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
8 weeks ago • updated 7 weeks ago altintas.ali • 0
1
vote
2
replies
311
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
8 weeks ago Hongjian • 0
3
votes
3
replies
307
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
9 weeks ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
337
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 9 weeks ago by 52k • written 10 weeks ago by • 0
1
vote
1
reply
253
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 11 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
1
vote
2
replies
473
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 11 weeks ago by 43k • written 12 weeks ago by ▴ 10
0
votes
2
replies
368
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 11 weeks ago by 52k • written 12 weeks ago by • 0
1
vote
2
replies
335
views
Inconsistent result in edgeR
edgeR
3 months ago hiroko.ohmiya • 0
1
vote
1
reply
459
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 3 months ago by 52k • written 3 months ago by • 0
2
votes
9
replies
840
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 3 months ago by 52k • written 3 months ago by • 0
0
votes
3
replies
523
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 4 months ago by • 0
1
vote
1
reply
713
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 4 months ago by ★ 28k • written 4 months ago by • 0
0
votes
1
reply
391
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 4 months ago by 52k • written 4 months ago by • 0
3
votes
3
replies
584
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 4 months ago by 67k • written 4 months ago by ▴ 50
0
votes
4
replies
591
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 5 months ago by • 0
1
vote
8
replies
991
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 5 months ago by 52k • written 5 months ago by • 0
3
votes
5
replies
1.7k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 5 months ago by • 0 • written 9 months ago by ▴ 50
0
votes
4
replies
619
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
6 months ago vohara4 • 0
3
votes
6
replies
841
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
6 months ago JG13 • 0
3
votes
2
replies
678
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
7 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
729
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 7 months ago by 52k • written 7 months ago by • 0
1
vote
3
replies
655
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 7 months ago by 52k • written 7 months ago by • 0
0
votes
1
reply
395
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 7 months ago by 52k • written 7 months ago by • 0
4
votes
2
replies
1.1k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
7 months ago gene_bioconductor ▴ 10
1
vote
2
replies
791
views
Citation for edgeR user guide
edgeR
written 7 months ago by ▴ 30
4
votes
6
replies
1.0k
views
FilterByExpr low counts with small sample size
edgeR
8 months ago Jonathan ▴ 10
0
votes
2
replies
397
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
8 months ago prity6459 • 0
0
votes
3
replies
583
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 8 months ago by 52k • written 8 months ago by • 0
5
votes
3
replies
918
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 months ago by 52k • written 8 months ago by • 0
3
votes
3
replies
927
views
permutation test in edgeR
rna-seq edgeR
updated 8 months ago by 52k • written 8 months ago by • 0
1
vote
3
replies
649
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 8 months ago by 52k • written 8 months ago by • 0
5
votes
6
replies
884
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 8 months ago by ★ 4.6k • written 8 months ago by ▴ 70
1
vote
3
replies
558
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 8 months ago by 67k • written 8 months ago by • 0
0
votes
2
replies
545
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
8 months ago Marianna ▴ 20
0
votes
4
replies
879
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
8 months ago Lucy ▴ 60
3
votes
5
replies
1.3k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 8 months ago by 52k • written 8 months ago by • 0
0
votes
6
replies
744
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 8 months ago by 52k • written 8 months ago by • 0
0
votes
1
reply
614
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 9 months ago by 52k • written 9 months ago by • 0
6
votes
5
replies
1.8k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 7 weeks ago by 52k • written 9 months ago by ▴ 50
2
votes
3
replies
611
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 9 months ago by 52k • written 9 months ago by • 0
0
votes
2
replies
579
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 months ago by 52k • written 9 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you James, that really helped! I tried CODE `enter code here` but I must have dome it incorrectly, as it showed all in red.
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k
Please come back to the support site and view your post - I've fixed it for you. If you want to show people your targets file, just paste t…
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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