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2
votes
1
answer
91
views
1
answer
Identify up and down regulated genes in affymetrix data
microarray affy limma written 18 hours ago by j_jamal96 • 0 • updated 8 hours ago by Gordon Smyth ♦ 30k
4
votes
2
answers
51
views
2
answers
Designing a model matrix and further process?
annotation limma process R written 1 day ago by Biotechuos4 • 0
5
votes
2
answers
112
views
2
answers
Volcanoplot with limma - RAW P-values or Adj.P-Values
limma volcanoplot fdr written 3 days ago by thyagoleal • 20 • updated 1 day ago by Wolfgang Huber ♦ 13k
0
votes
1
answer
68
views
1
answer
confusion with tximport options and resulting matrix
rnaseq limma voom tximport rsem written 2 days ago by arubio • 0 • updated 2 days ago by Gordon Smyth ♦ 30k
1
vote
1
answer
69
views
1
answer
Error from eBayes in limma package
limma error ebayes written 2 days ago by calen.p.ryan • 0 • updated 2 days ago by James W. MacDonald ♦ 43k
3
votes
4
answers
2.7k
views
4
answers
Volcano plot labeling troubles
limma volcanoplot written 2.7 years ago by mccallionc403 • 0 • updated 3 days ago by Gordon Smyth ♦ 30k
1
vote
1
answer
65
views
1
answer
Paired t-test with 2 groups, how to I tell the DEGs between them?
limma written 3 days ago by chris86 • 290 • updated 3 days ago by James W. MacDonald ♦ 43k
1
vote
2
answers
76
views
2
answers
Does LIMMA accept as an input "variance Stabilizing Transformation" generated by DSEQ
limma vst written 4 days ago by harelarik • 0 • updated 4 days ago by Gordon Smyth ♦ 30k
2
votes
3
answers
3.1k
views
3
answers
Limma: how to get same output as topTable but for all the genes ?
limma toptable written 8.7 years ago by Daren Tan • 150 • updated 5 days ago by Gordon Smyth ♦ 30k
7
votes
1
answer
180
views
1
answer
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq limma R logfc differential gene expression written 6 days ago by cms72 • 0 • updated 6 days ago by Aaron Lun • 15k
4
votes
1
answer
73
views
1
answer
Multi-level experiment with limma
regression limma design and contrast matrix differential gene expression written 8 days ago by luca.piacentini • 0 • updated 8 days ago by Aaron Lun • 15k
4
votes
1
answer
156
views
1
answer
Question about decideTests function and adj.p.value in "limma" R Package
limma R differential gene expression written 9 days ago by ghk • 0 • updated 9 days ago by Gordon Smyth ♦ 30k
3
votes
2
answers
78
views
2
answers
Limma validity for only hundreds of genes/metabolites
limma moderated t-test metabolite data written 12 days ago by iglezer • 0 • updated 12 days ago by Aaron Lun • 15k
0
votes
1
answer
103
views
1
answer
prior.prob has opposite effects in goana and kegga?
limma goana kegga missmethyl gometh written 10 weeks ago by Jenny Drnevich • 1.9k • updated 13 days ago by Gordon Smyth ♦ 30k
3
votes
2
answers
77
views
2
answers
Accounting for both categorical and numerical possible confounding variables in the limmaVoom pipeline
limma duplicatecorrelation limma voom written 16 days ago by lrutter0306 • 0
0
votes
1
answer
64
views
1
answer
bug in kegga() when using prior.prob?
limma edger written 15 days ago by Jenny Drnevich • 1.9k • updated 14 days ago by Gordon Smyth ♦ 30k
1
vote
1
answer
84
views
1
answer
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem written 14 days ago by ghk • 0 • updated 14 days ago by James W. MacDonald ♦ 43k
0
votes
2
answers
271
views
2
answers
base of B-value log in Limma
cancer limma written 11.2 years ago by Richard Friedman • 2.0k • updated 15 days ago by Gordon Smyth ♦ 30k
0
votes
1
answer
610
views
1
answer
[Limma] Using P value or B statistics for cutoff?
limma written 12.4 years ago by Wu, Xiwei • 350 • updated 15 days ago by Gordon Smyth ♦ 30k
3
votes
1
answer
54
views
1
answer
RankProd throws "is.infinite(data)" error for type "S4" for differential expression analysis
microarray affy limma rankprod bioconductor written 16 days ago by Tina Chapman • 20 • updated 16 days ago by James W. MacDonald ♦ 43k
7
votes
3
answers
589
views
5 follow
3
answers
Help with design matrix for two cell types, multiple treatments
limma deseq2 design and contrast matrix written 20 months ago by Jake • 50 • updated 17 days ago by alexis.maizel • 0
2
votes
2
answers
82
views
2
answers
Three way-interaction on voom (limma) data, including a factor with > 2 levels
rnaseq limma anova voom written 24 days ago by David Rengel • 60
1
vote
1
answer
77
views
1
answer
differentially expressed genes without contrasts
limma toptable makecontrasts contrast matrix written 24 days ago by hoe • 0 • updated 24 days ago by Ryan C. Thompson ♦ 5.8k
5
votes
1
answer
104
views
1
answer
Modeling input data in ChIP-seq experiments with EdgeR, DESeq(2) or Limma
chipseq limma edger deseq2 written 24 days ago by k.vitting.seerup • 0 • updated 24 days ago by Aaron Lun • 15k
2
votes
1
answer
65
views
1
answer
using edgeR or limma for 5C data normalization
limma edger deseq2 written 25 days ago by Bogdan • 470 • updated 24 days ago by Aaron Lun • 15k
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