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0
votes
1
answer
22
views
1
answer
Remove "no_feature" and "alignment_not_unique" counts before using EdgeR or Deseq2
edger deseq2 written 1 day ago by cottrellka • 0 • updated 1 day ago by Gordon Smyth ♦ 35k
0
votes
1
answer
89
views
1
answer
EstimateDisp and glm
edger written 3 days ago by samoura48 • 0 • updated 3 days ago by Aaron Lun • 21k
2
votes
1
answer
54
views
1
answer
Help with multi-factored RNA-seq edgeR model
rnaseq edger interaction model design model written 6 days ago by cody0071 • 0 • updated 6 days ago by James W. MacDonald ♦ 48k
3
votes
1
answer
183
views
1
answer
Normalization for small non-coding RNA and multi-factor design
normalization limma edger limma voom written 9 days ago by yeles.konstantinos • 10 • updated 8 days ago by James W. MacDonald ♦ 48k
0
votes
1
answer
103
views
1
answer
Count filter for differential expression
limma edger counts written 10 days ago by kaur • 0 • updated 10 days ago by Gordon Smyth ♦ 35k
2
votes
1
answer
71
views
1
answer
edgeR. Known cancer genes are not differentially expressed?
edger tcga written 12 days ago by rina • 0 • updated 12 days ago by Aaron Lun • 21k
2
votes
1
answer
76
views
1
answer
edgeR DE analysis: single group combined factors or GLM with interaction term
edger glm written 15 days ago by jspmccain • 10 • updated 15 days ago by Aaron Lun • 21k
5
votes
1
answer
950
views
1
answer
non-integer counts for edgeR
edger written 6.6 years ago by Gordon Smyth ♦ 35k
0
votes
1
answer
66
views
1
answer
Setting up the design for paired analysis
limma edger paired design written 17 days ago by candida.vaz • 30 • updated 16 days ago by James W. MacDonald ♦ 48k
2
votes
2
answers
60
views
2
answers
Filtering, minimum sample number, and condition in edgeR
edger filtering written 19 days ago by rproendo • 0 • updated 19 days ago by Ryan C. Thompson ♦ 7.1k
3
votes
1
answer
61
views
1
answer
Correct usage of tximport counts in edgeR without offset matrix.
edger rna-seq tximport written 19 days ago by ttekath • 0 • updated 19 days ago by James W. MacDonald ♦ 48k
5
votes
2
answers
189
views
2
answers
edgeR paired samples with blocking
limma edger paired samples blocking written 27 days ago by anou • 0 • updated 24 days ago by Gordon Smyth ♦ 35k
2
votes
1
answer
69
views
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 28 days ago by sdalin • 0 • updated 28 days ago by Gordon Smyth ♦ 35k
1
vote
1
answer
75
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1
answer
edgeR: boxplot the expression of a gene in two conditions after glmFit
edger written 28 days ago by zoppoli pietro • 10 • updated 28 days ago by Aaron Lun • 21k
1
vote
1
answer
112
views
1
answer
EdgeR RNAseq -- best way to deal with random effects
rnaseq edger written 29 days ago by emb13 • 0 • updated 29 days ago by Aaron Lun • 21k
1
vote
1
answer
122
views
1
answer
shRNA-Seq analysis using edgeR
edger experimental design model.matrix shrnaseq written 5 weeks ago by Assa Yeroslaviz • 1.4k • updated 4 weeks ago by Aaron Lun • 21k
1
vote
1
answer
111
views
1
answer
Change default prior.count in glmFit() to match cpm(), aveLogCPM(), etc?
edger prior.count written 5 weeks ago by Jenny Drnevich • 1.9k • updated 5 weeks ago by Gordon Smyth ♦ 35k
4
votes
2
answers
97
views
2
answers
EdgeR applied to peptide screen: help!
edger calcnormfactors library size factor peptide screen written 5 weeks ago by oakhamwolf • 0 • updated 5 weeks ago by Gordon Smyth ♦ 35k
0
votes
1
answer
71
views
1
answer
edgeR 2-way ANOVA testing
edger anova written 6 weeks ago by martyna.broda • 0 • updated 6 weeks ago by Gordon Smyth ♦ 35k
3
votes
2
answers
124
views
2
answers
Method to get normalized counts in edgeR without cpm
normalization edger written 6 weeks ago by Pauline • 0 • updated 6 weeks ago by Gordon Smyth ♦ 35k
0
votes
1
answer
97
views
1
answer
RNAseq gene expression analysis in Personalized genomics
limma edger deseq2 tcga written 6 weeks ago by bioc.vkas • 0 • updated 6 weeks ago by Michael Love ♦ 20k
2
votes
2
answers
96
views
2
answers
EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
edger glmlrt() design matrix paired design glmqftest() written 6 weeks ago by oakhamwolf • 0
0
votes
1
answer
112
views
1
answer
Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger differential gene expression glmtreat written 7 weeks ago by svlachavas • 630 • updated 6 weeks ago by Gordon Smyth ♦ 35k
2
votes
1
answer
119
views
1
answer
p -values smaller than machine epsilon in edgeR
edger p values written 6 weeks ago by oscarf • 0 • updated 6 weeks ago by Gordon Smyth ♦ 35k
3
votes
1
answer
92
views
1
answer
EdgeR - blocking for multiple factors at once - Errors
edger multiple factor design blocked design written 6 weeks ago by DonnyB • 0 • updated 6 weeks ago by Aaron Lun • 21k
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