Showing : EdgeR • reset
1
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8
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1.8k
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 15 months ago by 53k • written 15 months ago by • 0
3
votes
5
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3.2k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 15 months ago by • 0 • written 19 months ago by ▴ 60
0
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4
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1.1k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
16 months ago vohara4 • 0
3
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6
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1.3k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
16 months ago JG13 • 0
3
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2
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1.2k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
16 months ago mohammedtoufiq91 ▴ 10
3
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3
replies
1.1k
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 17 months ago by 53k • written 17 months ago by • 0
1
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3
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1.0k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 17 months ago by 53k • written 17 months ago by • 0
0
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1
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610
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 17 months ago by 53k • written 17 months ago by • 0
4
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2
replies
1.7k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
17 months ago gene_bioconductor ▴ 10
1
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2
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1.5k
views
Citation for edgeR user guide
edgeR
written 17 months ago by ▴ 30
4
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6
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1.7k
views
FilterByExpr low counts with small sample size
edgeR
18 months ago • updated 17 months ago Jonathan ▴ 10
0
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2
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649
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
17 months ago prity6459 • 0
0
votes
3
replies
916
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 17 months ago by 53k • written 17 months ago by • 0
5
votes
3
replies
1.5k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 17 months ago by 53k • written 18 months ago by • 0
3
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3
replies
1.7k
views
permutation test in edgeR
rna-seq edgeR
updated 17 months ago by 53k • written 18 months ago by • 0
1
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3
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913
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 18 months ago by 53k • written 18 months ago by • 0
5
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6
replies
1.4k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by ▴ 70
1
vote
3
replies
832
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
0
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2
replies
887
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
18 months ago Marianna ▴ 20
0
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4
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1.4k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
18 months ago Lucy ▴ 60
3
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6
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2.2k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
written 18 months ago by • 0
0
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6
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1.2k
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 18 months ago by 53k • written 18 months ago by • 0
0
votes
1
reply
1.0k
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 18 months ago by 53k • written 18 months ago by • 0
8
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5
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3.1k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 11 months ago by 53k • written 18 months ago by ▴ 60
2
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3
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1.0k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 19 months ago by 53k • written 19 months ago by • 0
0
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2
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820
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 19 months ago by 53k • written 19 months ago by • 0
2
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2
replies
882
views
between lane normalization upper quantile
EDASeq edgeR
19 months ago elesofi • 0
2
votes
2
replies
777
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
19 months ago Sabiha ▴ 20
1
vote
3
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975
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 20 months ago by • 0
0
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1
reply
529
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 19 months ago by 53k • written 19 months ago by • 0
0
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11
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1.8k
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 19 months ago by 53k • written 19 months ago by • 0
0
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1
reply
685
views
ExactTest vs QLFTest
edgeR
updated 19 months ago by 53k • written 19 months ago by • 0
1
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7
replies
1.6k
views
Library size normalization in methylation count analysis
edgeR MethylationArray
updated 11 months ago by • 0 • written 19 months ago by • 0
2
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6
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985
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
20 months ago • updated 19 months ago tsl0026 • 0
5
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4
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1.0k
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
20 months ago • updated 19 months ago pl23 • 0
0
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8
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1.7k
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
20 months ago • updated 19 months ago Marianna ▴ 20
5
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2
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1.8k
views
How does one test for interactions in EdgeR?
edgeR
20 months ago pl23 • 0
0
votes
4
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851
views
Nested paired design
edgeR
20 months ago manduchi ▴ 10
1
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2
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1.1k
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
20 months ago mico • 0
2
votes
3
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1.0k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 20 months ago by 68k • written 20 months ago by • 0
4
votes
4
replies
908
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 20 months ago by 68k • written 21 months ago by • 0
6
votes
7
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1.2k
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
1
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8
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1.5k
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 20 months ago by 53k • written 20 months ago by • 0
0
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0
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908
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
20 months ago Jawahar • 0
2
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4
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2.1k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
20 months ago Sabiha ▴ 20
0
votes
3
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1.3k
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 20 months ago by 53k • written 21 months ago by • 0
3
votes
3
replies
1.9k
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
4
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9
replies
2.3k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
21 months ago Luca • 0
0
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1
reply
594
views
download problem
edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
0
votes
5
replies
1.4k
views
Help with model for differential expression analysis
DifferentialExpression edgeR
21 months ago • updated 20 months ago Lucy ▴ 60
2,031 results • Page 2 of 41
Recent ...
Replies
Comment: PCA subset of genes vs DE by Ben • 0
PCA evaluates separation according to your input. The subset of genes you used may be entirely identical in terms of expression, indicatin…
Comment: Problem with MakeTxDbFromGFF by Ben • 0
Wow can't believe he can really answer this [speed stars][1] [1]: https://speed-stars.co
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.
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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