Showing : edger • reset
3
votes
3
replies
1.1k
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 17 months ago by 68k • written 17 months ago by ▴ 60
0
votes
4
replies
1.1k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 18 months ago by • 0
1
vote
8
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2.0k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 18 months ago by 53k • written 18 months ago by • 0
3
votes
5
replies
3.6k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 18 months ago by • 0 • written 22 months ago by ▴ 60
0
votes
4
replies
1.3k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
19 months ago vohara4 • 0
3
votes
6
replies
1.4k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
19 months ago JG13 • 0
3
votes
2
replies
1.3k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
19 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
1.2k
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
1
vote
3
replies
1.1k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
1
reply
674
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
4
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2
replies
1.8k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
20 months ago gene_bioconductor ▴ 10
1
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2
replies
1.8k
views
Citation for edgeR user guide
edgeR
written 20 months ago by ▴ 30
4
votes
6
replies
1.9k
views
FilterByExpr low counts with small sample size
edgeR
21 months ago • updated 20 months ago Jonathan ▴ 10
0
votes
2
replies
743
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
20 months ago prity6459 • 0
0
votes
3
replies
1.0k
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 20 months ago by 53k • written 20 months ago by • 0
5
votes
3
replies
1.6k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 20 months ago by 53k • written 21 months ago by • 0
3
votes
3
replies
1.9k
views
permutation test in edgeR
rna-seq edgeR
updated 20 months ago by 53k • written 21 months ago by • 0
1
vote
3
replies
993
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 21 months ago by 53k • written 21 months ago by • 0
5
votes
6
replies
1.6k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 21 months ago by ★ 5.0k • written 21 months ago by ▴ 70
1
vote
3
replies
957
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
2
replies
987
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
21 months ago Marianna ▴ 20
0
votes
4
replies
1.6k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
21 months ago Lucy ▴ 60
3
votes
6
replies
2.4k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
written 21 months ago by • 0
0
votes
6
replies
1.4k
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
0
votes
1
reply
1.2k
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
8
votes
5
replies
3.5k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 14 months ago by 53k • written 21 months ago by ▴ 60
2
votes
3
replies
1.1k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 22 months ago by 53k • written 22 months ago by • 0
0
votes
2
replies
906
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 22 months ago by 53k • written 22 months ago by • 0
2
votes
2
replies
997
views
between lane normalization upper quantile
EDASeq edgeR
22 months ago elesofi • 0
2
votes
2
replies
892
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
22 months ago Sabiha ▴ 20
1
vote
3
replies
1.1k
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 23 months ago by • 0
0
votes
1
reply
580
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
0
votes
11
replies
2.0k
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 22 months ago by 53k • written 22 months ago by • 0
0
votes
1
reply
730
views
ExactTest vs QLFTest
edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
1
vote
7
replies
1.8k
views
Library size normalization in methylation count analysis
edgeR MethylationArray
updated 14 months ago by • 0 • written 22 months ago by • 0
2
votes
6
replies
1.1k
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
23 months ago • updated 22 months ago tsl0026 • 0
5
votes
4
replies
1.1k
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
23 months ago • updated 22 months ago pl23 • 0
0
votes
8
replies
1.9k
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
23 months ago • updated 22 months ago Marianna ▴ 20
5
votes
2
replies
1.9k
views
How does one test for interactions in EdgeR?
edgeR
23 months ago pl23 • 0
0
votes
4
replies
965
views
Nested paired design
edgeR
23 months ago manduchi ▴ 10
1
vote
2
replies
1.2k
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
23 months ago mico • 0
2
votes
3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 23 months ago by 68k • written 23 months ago by • 0
4
votes
4
replies
1.0k
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 23 months ago by 68k • written 24 months ago by • 0
6
votes
7
replies
1.3k
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 23 months ago by 53k • written 23 months ago by • 0
1
vote
8
replies
1.6k
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 23 months ago by 53k • written 23 months ago by • 0
0
votes
0
replies
981
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
23 months ago Jawahar • 0
2
votes
4
replies
2.5k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
23 months ago Sabiha ▴ 20
0
votes
3
replies
1.4k
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 23 months ago by 53k • written 24 months ago by • 0
3
votes
3
replies
2.0k
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 24 months ago by 53k • written 24 months ago by • 0
4
votes
9
replies
2.5k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
2.0 years ago • updated 24 months ago Luca • 0
2,033 results • Page 2 of 41
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Answer: Combining two proteomics datasets with limpa by Gordon Smyth 53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub? by jwp48 • 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
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A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
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