Showing : EdgeR • reset
1
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822
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Performing a one-sided test for differential expression analysis in edgeR
edgeR
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
votes
0
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943
views
Manually adjusting BCV for exactTest in edgeR based on plotBCV
edgeR
2.5 years ago f_rahmdani • 0
0
votes
1
reply
726
views
Differential express genes in one group across all time points
DESeq2 edgeR BP4RNAseq ensemblVEP
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
2
votes
2
replies
900
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How Can I Assess the Reliability of BCV (Square-Root Dispersion) in Non-Replicated Experiments for Differential Expression Analysis Using edgeR?
edgeR
2.5 years ago f_rahmdani • 0
2
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8
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4.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
2.5 years ago • updated 2.4 years ago Luis • 0
0
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1
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1.0k
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
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1
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644
views
Can a expressed gene dataset yielded after CPM be used in DESeq2 and EdgeR?
DESeq2 edgeR
updated 2.5 years ago by ★ 4.1k • written 2.5 years ago by • 0
1
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2
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951
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Performing DE analysis using edgeR for PhIP-seq data with multiple samples, some with some without replicates.
edgeR
2.5 years ago f_rahmdani • 0
3
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9
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3.3k
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Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
2.5 years ago mohammedtoufiq91 ▴ 10
0
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2
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2.0k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.6 years ago Giulia • 0
0
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0
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800
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.6 years ago Giulia • 0
0
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0
replies
751
views
Plot profiles for each group - spline analysis in edgeR
timecoursedata edgeR
updated 2.6 years ago by 53k • written 2.6 years ago by ▴ 740
3
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1
reply
837
views
How edgeR estimate the common dispersion?
edgeR
2.6 years ago Dan • 0
1
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4
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2.6k
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How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 2.6 years ago by 53k • written 2.6 years ago by ▴ 10
3
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20
replies
3.6k
views
Time-course, comparison of two groups
edgeR
2.6 years ago • updated 2.5 years ago boczniak767 ▴ 740
0
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0
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734
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Limma: Models containing an intercept and interactions with continuous variables.
limma edgeR DifferentialExpression
2.6 years ago Aashil • 0
0
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5
replies
1.6k
views
hill-shaped p-value distributions using EdgeR
edgeR p-valuedistribution RNAseq hill-shaped
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
1
vote
2
replies
1.1k
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Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
2.6 years ago Yang Shi ▴ 10
1
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4
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1.3k
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
2.6 years ago DH • 0
4
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5
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2.8k
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Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.6 years ago by ▴ 760 • written 2.6 years ago by ▴ 10
0
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2
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1.1k
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Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma RNASeqData edgeR
updated 2.6 years ago by ▴ 40 • written 2.6 years ago by • 0
2
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5
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2.6k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 2.6 years ago by • 0
0
votes
3
replies
1.4k
views
Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
2
votes
6
replies
1.2k
views
Design matrix for analyzing time points
edgeR
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
3
votes
3
replies
1.2k
views
What is cpmByGroup used for?
edgeR Normalization
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
0
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2
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1.3k
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Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?
PrincipalComponent StatisticalMethod edgeR MultidimensionalScaling Normalization
2.6 years ago rcreswell01 • 0
2
votes
8
replies
2.2k
views
Help with inspecting DEs from QLF test and LRT
edgeR
2.6 years ago Tanner • 0
1
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1
reply
1.3k
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
6
votes
11
replies
2.3k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.7 years ago mohammedtoufiq91 ▴ 10
0
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1
reply
1.1k
views
Differential expression analysis with global differences among samples (tissues)
DESeq2 qsmooth edgeR limma
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
1
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1
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1.4k
views
Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 2.7 years ago by ★ 13k • written 2.7 years ago by ▴ 70
2
votes
2
replies
951
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fomulation of contrasts for blocked design
edgeR
2.7 years ago chaco001 • 0
6
votes
10
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4.0k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 18 months ago by • 0 • written 2.7 years ago by ▴ 10
1
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1
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1.2k
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
2
votes
1
reply
751
views
EdgeR model matrix
edgeR RNASeq
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
2
votes
10
replies
1.8k
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
3
votes
5
replies
1.6k
views
Design for DE analysis in tidybulk
DESeq2 designmatrix edgeR limma tidybulk
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 10
0
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1
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1.2k
views
Subset count data in DGEList using edgeR/DESeq2
edgeR DMR
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
3
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2
replies
1.0k
views
Help with the design matrix for longitudinal study
edgeR
2.7 years ago sharvari gujja ▴ 40
1
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3
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1.4k
views
Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 2.7 years ago by 43k • written 2.8 years ago by • 0
0
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2
replies
1.2k
views
Orange point meaning in plotSmear with edgeR
edgeR plotSmear
2.7 years ago Tess • 0
0
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3
replies
1.3k
views
Differential gene expression analysis with data matrix generated with RSEM
DESeq2 edgeR
2.8 years ago ubjw24 • 0
1
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1
reply
932
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
1
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1
reply
1.3k
views
Extracting the tophits from limma Volcanoplot and issue with geneIDs
limma edgeR Glimma
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
2
votes
5
replies
1.8k
views
Create the design matrix
DEGseq edgeR RNASeq
2.8 years ago Mohammad • 0
0
votes
2
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863
views
suggest to report differential estimate in edgeR
edgeR
2.8 years ago • updated 2.7 years ago Yongqing • 0
0
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4
replies
1.3k
views
What function in edgeR normalize the reads between samples?
edgeR
2.8 years ago 冠宇 • 0
4
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5
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6.4k
views
How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
updated 2.7 years ago by 53k • written 2.8 years ago by ▴ 10
2
votes
2
replies
981
views
Inccorect group number in DGEList
edgeR Bioconductor Dseq2 dgelist
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
0
votes
0
replies
822
views
Installing edgeR on M1 mac
edgeR
2.8 years ago Onur • 0
2,031 results • Page 4 of 41
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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