Showing : edger • reset
3
votes
2
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1.1k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
15 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
1.1k
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 15 months ago by 52k • written 15 months ago by • 0
1
vote
3
replies
987
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 15 months ago by 52k • written 15 months ago by • 0
0
votes
1
reply
589
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 16 months ago by 52k • written 16 months ago by • 0
4
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2
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1.7k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
16 months ago gene_bioconductor ▴ 10
1
vote
2
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1.5k
views
Citation for edgeR user guide
edgeR
written 16 months ago by ▴ 30
4
votes
6
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1.6k
views
FilterByExpr low counts with small sample size
edgeR
16 months ago Jonathan ▴ 10
0
votes
2
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624
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
16 months ago prity6459 • 0
0
votes
3
replies
882
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 16 months ago by 52k • written 16 months ago by • 0
5
votes
3
replies
1.5k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 16 months ago by 52k • written 16 months ago by • 0
3
votes
3
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1.7k
views
permutation test in edgeR
rna-seq edgeR
updated 16 months ago by 52k • written 17 months ago by • 0
1
vote
3
replies
882
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 16 months ago by 52k • written 17 months ago by • 0
5
votes
6
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1.4k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 16 months ago by ★ 4.9k • written 17 months ago by ▴ 70
1
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3
replies
797
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
0
votes
2
replies
846
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
17 months ago Marianna ▴ 20
0
votes
4
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1.3k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
17 months ago Lucy ▴ 60
3
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6
replies
2.1k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
written 17 months ago by • 0
0
votes
6
replies
1.2k
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 17 months ago by 52k • written 17 months ago by • 0
0
votes
1
reply
990
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 17 months ago by 52k • written 17 months ago by • 0
8
votes
5
replies
3.0k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 10 months ago by 52k • written 17 months ago by ▴ 60
2
votes
3
replies
980
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 17 months ago by 52k • written 17 months ago by • 0
0
votes
2
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791
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 17 months ago by 52k • written 17 months ago by • 0
2
votes
2
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858
views
between lane normalization upper quantile
EDASeq edgeR
17 months ago elesofi • 0
2
votes
2
replies
743
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
17 months ago Sabiha ▴ 20
1
vote
3
replies
947
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 19 months ago by • 0
0
votes
1
reply
515
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 18 months ago by 52k • written 18 months ago by • 0
0
votes
11
replies
1.7k
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 18 months ago by 52k • written 18 months ago by • 0
0
votes
1
reply
666
views
ExactTest vs QLFTest
edgeR
updated 18 months ago by 52k • written 18 months ago by • 0
1
vote
7
replies
1.6k
views
Library size normalization in methylation count analysis
edgeR MethylationArray
updated 10 months ago by • 0 • written 18 months ago by • 0
2
votes
6
replies
952
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
18 months ago tsl0026 • 0
5
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4
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964
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
18 months ago pl23 • 0
0
votes
8
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1.6k
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
19 months ago • updated 18 months ago Marianna ▴ 20
5
votes
2
replies
1.7k
views
How does one test for interactions in EdgeR?
edgeR
19 months ago • updated 18 months ago pl23 • 0
0
votes
4
replies
822
views
Nested paired design
edgeR
19 months ago manduchi ▴ 10
1
vote
2
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1.0k
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
19 months ago mico • 0
2
votes
3
replies
988
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 19 months ago by 68k • written 19 months ago by • 0
4
votes
4
replies
876
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 19 months ago by 68k • written 20 months ago by • 0
6
votes
7
replies
1.2k
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 19 months ago by 52k • written 19 months ago by • 0
1
vote
8
replies
1.4k
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 19 months ago by 52k • written 19 months ago by • 0
0
votes
0
replies
889
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
19 months ago Jawahar • 0
2
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4
replies
2.0k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
19 months ago Sabiha ▴ 20
0
votes
3
replies
1.2k
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 19 months ago by 52k • written 19 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 19 months ago by 52k • written 19 months ago by • 0
4
votes
9
replies
2.3k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
20 months ago • updated 19 months ago Luca • 0
0
votes
1
reply
579
views
download problem
edgeR
updated 20 months ago by 52k • written 20 months ago by • 0
0
votes
5
replies
1.3k
views
Help with model for differential expression analysis
DifferentialExpression edgeR
20 months ago • updated 19 months ago Lucy ▴ 60
1
vote
2
replies
1.2k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
20 months ago Sabiha ▴ 20
5
votes
2
replies
1.4k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 21 months ago by 52k • written 21 months ago by • 0
1
vote
2
replies
1.3k
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 21 months ago by 52k • written 21 months ago by • 0
12
votes
5
replies
4.7k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 3 months ago by • 0 • written 21 months ago by • 0
2,027 results • Page 2 of 41
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Comment: EuroBioC2024 abstract submission is open! by Finnianfly • 0
What specific requirements should be noted when preparing abstracts for presentation formats such as short talks, package demos, or posters…
Comment: Length of 'dimnames' [1] not equal to array extent by Francesco Silvestro • 0
Resolved the error message!
Comment: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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