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0
votes
1
answer
74
views
1
answer
Count filter for differential expression
limma edger counts written 1 day ago by kaur • 0 • updated 8 hours ago by Gordon Smyth ♦ 35k
1
vote
1
answer
40
views
1
answer
edgeR. Known cancer genes are not differentially expressed?
edger tcga written 3 days ago by rina • 0 • updated 2 days ago by Aaron Lun • 21k
1
vote
1
answer
57
views
1
answer
edgeR DE analysis: single group combined factors or GLM with interaction term
edger glm written 5 days ago by jspmccain • 10 • updated 5 days ago by Aaron Lun • 21k
5
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1
answer
932
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1
answer
non-integer counts for edgeR
edger written 6.6 years ago by Gordon Smyth ♦ 35k
0
votes
1
answer
57
views
1
answer
Setting up the design for paired analysis
limma edger paired design written 7 days ago by candida.vaz • 30 • updated 6 days ago by James W. MacDonald ♦ 48k
2
votes
2
answers
53
views
2
answers
Filtering, minimum sample number, and condition in edgeR
edger filtering written 9 days ago by rproendo • 0 • updated 9 days ago by Ryan C. Thompson ♦ 7.0k
3
votes
1
answer
45
views
1
answer
Correct usage of tximport counts in edgeR without offset matrix.
edger rna-seq tximport written 9 days ago by ttekath • 0 • updated 9 days ago by James W. MacDonald ♦ 48k
5
votes
2
answers
166
views
2
answers
edgeR paired samples with blocking
limma edger paired samples blocking written 18 days ago by anou • 0 • updated 14 days ago by Gordon Smyth ♦ 35k
2
votes
1
answer
61
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1
answer
EdgeR: With two treatments, is it equivalent to split into two different models vs. making the relevant pairwise comparisons?
edger contrast design matrix written 18 days ago by sdalin • 0 • updated 18 days ago by Gordon Smyth ♦ 35k
1
vote
1
answer
66
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1
answer
edgeR: boxplot the expression of a gene in two conditions after glmFit
edger written 18 days ago by zoppoli pietro • 10 • updated 18 days ago by Aaron Lun • 21k
1
vote
1
answer
98
views
1
answer
EdgeR RNAseq -- best way to deal with random effects
rnaseq edger written 19 days ago by emb13 • 0 • updated 19 days ago by Aaron Lun • 21k
1
vote
1
answer
116
views
1
answer
shRNA-Seq analysis using edgeR
edger experimental design model.matrix shrnaseq written 25 days ago by Assa Yeroslaviz • 1.4k • updated 25 days ago by Aaron Lun • 21k
1
vote
1
answer
94
views
1
answer
Change default prior.count in glmFit() to match cpm(), aveLogCPM(), etc?
edger prior.count written 4 weeks ago by Jenny Drnevich • 1.9k • updated 27 days ago by Gordon Smyth ♦ 35k
4
votes
2
answers
86
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2
answers
EdgeR applied to peptide screen: help!
edger calcnormfactors library size factor peptide screen written 4 weeks ago by oakhamwolf • 0 • updated 4 weeks ago by Gordon Smyth ♦ 35k
0
votes
1
answer
65
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1
answer
edgeR 2-way ANOVA testing
edger anova written 4 weeks ago by martyna.broda • 0 • updated 4 weeks ago by Gordon Smyth ♦ 35k
3
votes
2
answers
111
views
2
answers
Method to get normalized counts in edgeR without cpm
normalization edger written 4 weeks ago by Pauline • 0 • updated 4 weeks ago by Gordon Smyth ♦ 35k
0
votes
1
answer
91
views
1
answer
RNAseq gene expression analysis in Personalized genomics
limma edger deseq2 tcga written 5 weeks ago by bioc.vkas • 0 • updated 4 weeks ago by Michael Love ♦ 20k
2
votes
2
answers
90
views
2
answers
EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
edger glmlrt() design matrix paired design glmqftest() written 5 weeks ago by oakhamwolf • 0
0
votes
1
answer
106
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1
answer
Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger differential gene expression glmtreat written 6 weeks ago by svlachavas • 610 • updated 5 weeks ago by Gordon Smyth ♦ 35k
2
votes
1
answer
107
views
1
answer
p -values smaller than machine epsilon in edgeR
edger p values written 5 weeks ago by oscarf • 0 • updated 5 weeks ago by Gordon Smyth ♦ 35k
3
votes
1
answer
84
views
1
answer
EdgeR - blocking for multiple factors at once - Errors
edger multiple factor design blocked design written 5 weeks ago by DonnyB • 0 • updated 5 weeks ago by Aaron Lun • 21k
1
vote
1
answer
140
views
1
answer
edgeR package fails to load after install
edger install error written 5 weeks ago by jenny.russ • 0 • updated 5 weeks ago by Aaron Lun • 21k
2
votes
1
answer
109
views
1
answer
Predict circadian expression with edgeR
edger circadian rhythms limorhyde written 5 weeks ago by ri.lars • 40 • updated 5 weeks ago by Aaron Lun • 21k
2
votes
1
answer
102
views
1
answer
Multi-factor with interaction model in EdgeR and DESeq2
rnaseq edger deseq2 differential gene expression written 5 weeks ago by camilla.alves • 0 • updated 5 weeks ago by Michael Love ♦ 20k
9
votes
2
answers
149
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5 follow
2
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Finding DE genes from RNA-seq data
qvalue edger differential gene expression fpkm pvalue written 6 weeks ago by Harrisonesmith • 0 • updated 6 weeks ago by Steve Lianoglou ♦ 12k
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