Showing : edger • reset
1
vote
8
replies
491
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
updated 1 day ago by 52k • written 2 days 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 10 days ago by ★ 4.6k • written 22 days ago by ▴ 10
7
votes
6
replies
841
views
ANOVA like approach of edgeR
edgeR
updated 22 days ago by 52k • written 27 days ago by ▴ 10
3
votes
3
replies
529
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 29 days ago by 52k • written 29 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 6 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
619
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
312
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
9 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 10 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
370
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
337
views
Inconsistent result in edgeR
edgeR
3 months ago hiroko.ohmiya • 0
1
vote
1
reply
460
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
842
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
719
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
393
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
593
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
999
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 6 months ago by • 0 • written 9 months ago by ▴ 50
0
votes
4
replies
621
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
842
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
656
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
396
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
797
views
Citation for edgeR user guide
edgeR
written 8 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
587
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
923
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
931
views
permutation test in edgeR
rna-seq edgeR
updated 8 months ago by 52k • written 8 months ago by • 0
1
vote
3
replies
650
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
885
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
560
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
546
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
8 months ago Marianna ▴ 20
0
votes
4
replies
882
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
748
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
616
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
612
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
581
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 xiaofeiwang198266 • 0
Thanks for your reply!
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Hervé Pagès 16k
> I have requested gDNAx developers for a feature request to turn off seqlevelsStyle(txdb) Yes, that's the right course of action. `seqlev…
Comment: ISO a solution to rank-order introns by transcript by mat149 ▴ 80
Hey, In revisiting this question, the following code works for the '+' strand. I am having issues with demarcating intron rank by transcri…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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