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0
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1
answer
68
views
1
answer
DESeq2 biological replicates and RIN values
rnaseq deseq2 differential gene expression covariates written 4 days ago by pmoranlosada • 0 • updated 2 days ago by Michael Love ♦ 13k
1
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39
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Differential expression of nomalised and log2 transformed data in limma
limma differential gene expression lmfit model.matrix written 2 days ago by stinehedensted • 0
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1
answer
63
views
1
answer
Does edgeR accept decimal / integer read counts for differential expression ?
edger differential gene expression written 6 days ago by Padhmanand.Sudhakar • 0 • updated 6 days ago by Gordon Smyth ♦ 31k
0
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1
answer
240
views
1
answer
Paired Difference Analysis
deseq2 R differential gene expression written 5 weeks ago by nhua • 0
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2
answers
147
views
2
answers
Choosing genes for clustering
clustering limma differential gene expression feature selection hierarchical clustering written 11 days ago by lirongrossmann • 0 • updated 6 days ago by Gordon Smyth ♦ 31k
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0
answers
82
views
0
answers
Combined strand specific and unstranded samples
rnaseq strand counts differential gene expression batch effect written 10 days ago by lirongrossmann • 0
3
votes
1
answer
114
views
1
answer
How do you test a contrast in MAST?
differential gene expression single-cell mast written 10 days ago by Shian Su • 10 • updated 10 days ago by Andrew_McDavid • 80
2
votes
1
answer
113
views
1
answer
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 differential gene expression wald lrt written 12 days ago by chrysanthi.taxiarchi12 • 0 • updated 11 days ago by Gavin Kelly • 320
7
votes
2
answers
195
views
2
answers
Limma and batch effect
clustering limma differential gene expression removebatcheffect written 13 days ago by lirongrossmann • 0 • updated 12 days ago by Gordon Smyth ♦ 31k
0
votes
1
answer
252
views
1
answer
DEseq package statistical test
deseq2 differential gene expression written 25 days ago by rohan bareja • 200 • updated 25 days ago by Steve Lianoglou ♦ 12k
1
vote
1
answer
329
views
1
answer
DESEq2 p-values weird distribution under the H0 and fdrtool
rnaseq deseq2 differential gene expression fdrtool written 4 weeks ago by thyagoleal • 20
1
vote
1
answer
307
views
1
answer
design contrast in limma package for microarray expression data
limma design and contrast matrix differential gene expression written 4 weeks ago by sup230 • 10 • updated 4 weeks ago by Aaron Lun • 16k
1
vote
1
answer
382
views
1
answer
Why Differential expression results differ with edgeR and limma ?
limma edger R differential gene expression written 4 weeks ago by ghk • 0
2
votes
1
answer
335
views
1
answer
decideTests error with edgeR package
edger R differential gene expression written 4 weeks ago by ghk • 0 • updated 4 weeks ago by Aaron Lun • 16k
0
votes
0
answers
344
views
0
answers
Ballgown with replicates and the adjustvars option
rnaseq differential gene expression ballgown written 5 weeks ago by o.diogosilva • 0
3
votes
1
answer
385
views
1
answer
Filtering step in Differential analysis with RSEM values
edger differential gene expression rsem written 5 weeks ago by ghk • 0 • updated 5 weeks ago by Gordon Smyth ♦ 31k
0
votes
1
answer
356
views
1
answer
NAs in continuous coefficient and fold change in `zlm`
differential gene expression scrnaseq mast written 5 weeks ago by Andrew_McDavid • 80
1
vote
1
answer
445
views
1
answer
Finding the correct covariate for RNAseq experiment
sva deseq2 differential gene expression removebatcheffect() written 6 weeks ago by mat.lesche • 10 • updated 6 weeks ago by Michael Love ♦ 13k
1
vote
2
answers
282
views
2
answers
edgeR in a situation with unbalanced design: to include only subjects with matching time points or not?
edger differential gene expression written 7 weeks ago by cafelumiere12 • 20 • updated 6 weeks ago by Gordon Smyth ♦ 31k
7
votes
1
answer
690
views
1
answer
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq limma R logfc differential gene expression written 9 weeks ago by cms72 • 0 • updated 9 weeks ago by Aaron Lun • 16k
3
votes
2
answers
128
views
2
answers
Does DEseq2 analysis make GOseq redundant?
goseq deseq2 gene ontology differential gene expression written 9 weeks ago by david.rinker • 0
0
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0
answers
99
views
0
answers
design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
design and contrast matrix differential gene expression nanostring nanostringdiff ncounter written 9 weeks ago by c.kohler • 0
4
votes
1
answer
113
views
1
answer
Multi-level experiment with limma
regression limma design and contrast matrix differential gene expression written 9 weeks ago by luca.piacentini • 0 • updated 9 weeks ago by Aaron Lun • 16k
4
votes
1
answer
224
views
1
answer
Question about decideTests function and adj.p.value in "limma" R Package
limma R differential gene expression written 9 weeks ago by ghk • 0 • updated 9 weeks ago by Gordon Smyth ♦ 31k
1
vote
1
answer
145
views
1
answer
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem written 10 weeks ago by ghk • 0 • updated 10 weeks ago by James W. MacDonald ♦ 44k
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