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3
votes
1
answer
59
views
1
answer
How to calculate average log2 CPM with batch effect?
limma edger cpm written 6 days ago by b.nota • 300 • updated 5 days ago by Aaron Lun • 21k
6
votes
1
answer
71
views
1
answer
edgeR compilation error: with g++ 4.9.2 and R-5.0 on linux platform
edger compilation error written 6 days ago by Pengcheng Yang • 50 • updated 6 days ago by Gordon Smyth ♦ 35k
2
votes
1
answer
58
views
1
answer
edgeR with related individuals?
edger design matrix related written 15 days ago by joanna.l.kelley • 0 • updated 15 days ago by James W. MacDonald ♦ 48k
3
votes
1
answer
61
views
1
answer
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
visualization clustering edger written 15 days ago by thindmarsmission • 0 • updated 15 days ago by James W. MacDonald ♦ 48k
1
vote
1
answer
59
views
1
answer
EdgeR between unequal group sizes?
rnaseq edger differential gene expression written 16 days ago by rina • 0 • updated 16 days ago by Gordon Smyth ♦ 35k
1
vote
1
answer
55
views
1
answer
EDASeq, RUVSeq and edgeR together
edger edaseq ruvseq written 20 days ago by zoppoli pietro • 10 • updated 19 days ago by davide risso • 750
1
vote
1
answer
69
views
1
answer
the results of logFC is base e (log(FC,base=exp(1)) or base 2 (log2FC) ,is logFC same as log2FC in edgeR?
limma edger logfc written 22 days ago by ZihaoXing • 0 • updated 21 days ago by Gordon Smyth ♦ 35k
2
votes
1
answer
104
views
1
answer
why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM_tumor_mean/FPKM_normal_mean)?
edger deseq2 counts fpkm fc written 24 days ago by ZihaoXing • 0 • updated 23 days ago by Gordon Smyth ♦ 35k
1
vote
1
answer
79
views
1
answer
how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?
edger deseq2 counts tcga fpkm written 23 days ago by ZihaoXing • 0 • updated 23 days ago by Gordon Smyth ♦ 35k
3
votes
1
answer
100
views
1
answer
use only lib size as normalizing factor in edgeR
edger written 24 days ago by Udi Landau • 30 • updated 24 days ago by Aaron Lun • 21k
2
votes
1
answer
113
views
1
answer
Correct formulation of contrasts of interest regarding an RNA-Seq gene expression analysis with edgeR
rnaseq edger design and contrast matrix multifactorial design written 29 days ago by fotakisg • 0 • updated 27 days ago by Aaron Lun • 21k
1
vote
1
answer
115
views
1
answer
can i only analyse some genes different RNAseq expression analyse not the whole transcriptome RNAseq analyse by DESeq2 or edgeR
edger deseq2 written 29 days ago by ZihaoXing • 0 • updated 29 days ago by Gordon Smyth ♦ 35k
2
votes
1
answer
161
views
1
answer
edgeR: design matrix for methylation analysis
edger methylation written 3 months ago by sgld • 0 • updated 29 days ago by Gordon Smyth ♦ 35k
1
vote
1
answer
94
views
1
answer
why the p value and FDR is different between classic exactTest and glm glmQLFTest in edgeR?
edger written 4 weeks ago by ZihaoXing • 0 • updated 4 weeks ago by James W. MacDonald ♦ 48k
4
votes
1
answer
97
views
1
answer
EdgeR blocking and "All combinations of multiple factors"
edger differential gene expression written 4 weeks ago by rfenouil • 0 • updated 4 weeks ago by James W. MacDonald ♦ 48k
8
votes
1
answer
73
views
1
answer
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect written 4 weeks ago by Laura • 20 • updated 4 weeks ago by Aaron Lun • 21k
2
votes
1
answer
98
views
1
answer
EdgeR analysis batch effect
edger differential gene expression written 4 weeks ago by rfenouil • 0 • updated 4 weeks ago by Aaron Lun • 21k
6
votes
1
answer
73
views
5 follow
1
answer
Pre-ranked camera gene set testing with edgeR results
limma edger camera gene set testing camerapr written 5 weeks ago by jamie.gearing • 40 • updated 4 weeks ago by Gordon Smyth ♦ 35k
1
vote
1
answer
100
views
1
answer
How do I discern if a magnitude difference in expression is up-regulation in one group or down-regulation in another?
edger R differential gene expression gene list up-regulation written 5 weeks ago by philip.freda • 0 • updated 5 weeks ago by Gordon Smyth ♦ 35k
3
votes
1
answer
104
views
1
answer
edgeR analysis of cells treated with either drug1, drug2, or a time matched control at two different time points, did I set this up correctly?
rnaseq edger bioinformatics gene expression written 5 weeks ago by brett.vanderwerff • 0 • updated 5 weeks ago by Gordon Smyth ♦ 35k
0
votes
1
answer
98
views
1
answer
RNA-seq unbalanced batch effect correction
rnaseq edger batch effect written 6 weeks ago by sckinta • 0 • updated 5 weeks ago by James W. MacDonald ♦ 48k
3
votes
1
answer
74
views
1
answer
DE genes comparison of different treatments from microarray and RNAseq data
microarray limma edger deseq2 written 7 weeks ago by Bio_Ram • 0 • updated 7 weeks ago by James W. MacDonald ♦ 48k
3
votes
2
answers
125
views
2
answers
CNV-expression testing with edgeR
edger written 7 weeks ago by Ludwig Geistlinger • 40
1
vote
1
answer
108
views
1
answer
EdgeR filtering, gene expression, cpm cutoff
edger tutorial written 7 weeks ago by ilovesuperheroes1993 • 0 • updated 7 weeks ago by Hotz, Hans-Rudolf • 400
3
votes
1
answer
172
views
1
answer
Error in glmFit.default() : y is not a numeric matrix
edger written 7 weeks ago by borpano • 20 • updated 7 weeks ago by Aaron Lun • 21k
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