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4
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2
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543
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
5 days ago • updated 1 day ago
gene_bioconductor
▴ 10
0
votes
1
reply
122
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 5 days ago by
Gordon Smyth
50k • written 5 days ago by
z_bahari
• 0
1
vote
1
reply
179
views
Citation for edgeR user guide
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
k___
▴ 30
0
votes
2
replies
137
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
18 days ago
prity6459
• 0
0
votes
3
replies
193
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 18 days ago by
Gordon Smyth
50k • written 19 days ago by
prity6459
• 0
3
votes
1
reply
179
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 18 days ago by
Gordon Smyth
50k • written 19 days ago by
Shaimaa Gamal
• 0
4
votes
6
replies
438
views
FilterByExpr low counts with small sample size
edgeR
20 days ago • updated 15 days ago
Jonathan
▴ 10
1
vote
3
replies
352
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 22 days ago by
Gordon Smyth
50k • written 27 days ago by
Simran
• 0
5
votes
6
replies
432
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 24 days ago by
ATpoint
★ 4.1k • written 28 days ago by
nhaus
▴ 30
3
votes
3
replies
340
views
permutation test in edgeR
rna-seq
edgeR
updated 16 days ago by
Gordon Smyth
50k • written 29 days ago by
Netanel
• 0
1
vote
3
replies
265
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Shaimaa Gamal
• 0
0
votes
2
replies
174
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
4 weeks ago
Marianna
▴ 20
0
votes
4
replies
433
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
5 weeks ago
Lucy
▴ 60
3
votes
5
replies
390
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Fabian
• 0
0
votes
6
replies
359
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Faisal
• 0
0
votes
1
reply
236
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
scoops_streams_06
• 0
5
votes
3
replies
714
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Jack S.
▴ 50
2
votes
3
replies
297
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
JKim
• 0
0
votes
2
replies
285
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
z_bahari
• 0
2
votes
2
replies
257
views
between lane normalization upper quantile
EDASeq
edgeR
7 weeks ago
elesofi
• 0
2
votes
2
replies
266
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
7 weeks ago
Sabiha
▴ 20
3
votes
4
replies
435
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 8 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Jack S.
▴ 50
0
votes
1
reply
223
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Fabian
• 0
0
votes
1
reply
258
views
ExactTest vs QLFTest
edgeR
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
fr8712ca-s
• 0
0
votes
11
replies
743
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 9 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
mico
• 0
1
vote
6
replies
496
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
10 weeks ago
mico
• 0
5
votes
4
replies
402
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
11 weeks ago • updated 10 weeks ago
pl23
• 0
2
votes
6
replies
419
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
11 weeks ago
tsl0026
• 0
0
votes
8
replies
643
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
12 weeks ago • updated 11 weeks ago
Marianna
▴ 20
3
votes
2
replies
445
views
How does one test for interactions in EdgeR?
edgeR
12 weeks ago
pl23
• 0
0
votes
4
replies
354
views
Nested paired design
edgeR
3 months ago
manduchi
▴ 10
1
vote
2
replies
328
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
3 months ago • updated 12 weeks ago
mico
• 0
2
votes
3
replies
372
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Shaimaa Gamal
• 0
1
vote
3
replies
412
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 3 months ago by
pl23
• 0
6
votes
7
replies
574
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
aa.machado001
• 0
1
vote
8
replies
551
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
sat
• 0
0
votes
0
replies
247
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
3 months ago
Jawahar
• 0
2
votes
4
replies
599
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
0
votes
3
replies
347
views
EdgeR for methylation analysis when there is no replicates
RRBSdata
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
annasoudi
• 0
3
votes
3
replies
684
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Jurgen
• 0
4
votes
4
replies
436
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Geo
• 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
4 months ago • updated 3 months ago
Luca
• 0
0
votes
1
reply
312
views
download problem
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 4 months ago by
theokirkland3
• 0
0
votes
5
replies
622
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
4 months ago • updated 3 months ago
Lucy
▴ 60
1
vote
2
replies
470
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
4 months ago
Sabiha
▴ 20
5
votes
2
replies
563
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
1
vote
2
replies
427
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
Jurgen
• 0
7
votes
2
replies
812
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
0
votes
3
replies
460
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
5 months ago
Karthik
• 0
4
votes
2
replies
640
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
alvaroperona1
▴ 10
50 results • Page
1 of 1
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Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
nbay13
• 0
A little late to the party, but I found that using the equation you specified, the p-values are actually slightly off from base R's `t.test…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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