Showing : EDGER • reset
1
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836
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Performing a one-sided test for differential expression analysis in edgeR
edgeR
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
0
votes
0
replies
956
views
Manually adjusting BCV for exactTest in edgeR based on plotBCV
edgeR
2.6 years ago f_rahmdani • 0
0
votes
1
reply
744
views
Differential express genes in one group across all time points
DESeq2 edgeR BP4RNAseq ensemblVEP
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
2
votes
2
replies
914
views
How Can I Assess the Reliability of BCV (Square-Root Dispersion) in Non-Replicated Experiments for Differential Expression Analysis Using edgeR?
edgeR
2.6 years ago f_rahmdani • 0
2
votes
8
replies
4.4k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
2.6 years ago • updated 2.4 years ago Luis • 0
0
votes
1
reply
1.0k
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
votes
1
reply
651
views
Can a expressed gene dataset yielded after CPM be used in DESeq2 and EdgeR?
DESeq2 edgeR
updated 2.6 years ago by ★ 4.1k • written 2.6 years ago by • 0
1
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2
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965
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Performing DE analysis using edgeR for PhIP-seq data with multiple samples, some with some without replicates.
edgeR
2.6 years ago f_rahmdani • 0
3
votes
9
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3.4k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
2.6 years ago mohammedtoufiq91 ▴ 10
0
votes
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
replies
817
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.6 years ago Giulia • 0
0
votes
0
replies
764
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
votes
1
reply
848
views
How edgeR estimate the common dispersion?
edgeR
2.7 years ago • updated 2.6 years ago Dan • 0
1
vote
4
replies
2.6k
views
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
votes
20
replies
3.6k
views
Time-course, comparison of two groups
edgeR
2.6 years ago boczniak767 ▴ 740
0
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0
replies
744
views
Limma: Models containing an intercept and interactions with continuous variables.
limma edgeR DifferentialExpression
2.6 years ago Aashil • 0
0
votes
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
1.2k
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
2.6 years ago Yang Shi ▴ 10
1
vote
4
replies
1.3k
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
2.6 years ago DH • 0
4
votes
5
replies
2.9k
views
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
replies
1.2k
views
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 2.7 years ago by ▴ 40 • written 2.7 years ago by • 0
2
votes
5
replies
2.7k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 2.7 years ago by • 0
0
votes
3
replies
1.4k
views
Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
2
votes
6
replies
1.2k
views
Design matrix for analyzing time points
edgeR
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
3
votes
3
replies
1.3k
views
What is cpmByGroup used for?
edgeR Normalization
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
0
votes
2
replies
1.4k
views
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
2.7 years ago rcreswell01 • 0
2
votes
8
replies
2.2k
views
Help with inspecting DEs from QLF test and LRT
edgeR
2.7 years ago Tanner • 0
1
vote
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
2.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.7 years ago mohammedtoufiq91 ▴ 10
0
votes
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
reply
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
964
views
fomulation of contrasts for blocked design
edgeR
2.7 years ago chaco001 • 0
6
votes
10
replies
4.1k
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
vote
1
reply
1.3k
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
762
views
EdgeR model matrix
edgeR RNASeq
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
2
votes
10
replies
1.9k
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
3
votes
5
replies
1.7k
views
Design for DE analysis in tidybulk
DESeq2 designmatrix edgeR limma tidybulk
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Subset count data in DGEList using edgeR/DESeq2
edgeR DMR
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
3
votes
2
replies
1.0k
views
Help with the design matrix for longitudinal study
edgeR
2.8 years ago sharvari gujja ▴ 40
1
vote
3
replies
1.4k
views
Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
votes
2
replies
1.2k
views
Orange point meaning in plotSmear with edgeR
edgeR plotSmear
2.8 years ago Tess • 0
0
votes
3
replies
1.3k
views
Differential gene expression analysis with data matrix generated with RSEM
DESeq2 edgeR
2.8 years ago ubjw24 • 0
1
vote
1
reply
990
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
vote
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
replies
875
views
suggest to report differential estimate in edgeR
edgeR
2.8 years ago Yongqing • 0
0
votes
4
replies
1.3k
views
What function in edgeR normalize the reads between samples?
edgeR
2.8 years ago 冠宇 • 0
4
votes
5
replies
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
1.0k
views
Inccorect group number in DGEList
edgeR Bioconductor Dseq2 dgelist
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
votes
0
replies
828
views
Installing edgeR on M1 mac
edgeR
2.9 years ago Onur • 0
2,031 results • Page 4 of 41
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
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
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Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
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