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edgeR
•
reset
25
votes
7
replies
12k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma
deseq2
edger
rnaseq
updated 7.6 years ago by
Gordon Smyth
52k • written 7.6 years ago by
Jack
▴ 20
25
votes
11
replies
8.7k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq
deseq2
edgeR
normalization
updated 9.4 years ago by
Simon Anders
★ 3.8k • written 9.4 years ago by
Nik Tuzov
▴ 90
25
votes
37
replies
13k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq
RSEM
TCGA
edgeR
normalization
updated 8.3 years ago by
Gordon Smyth
52k • written 8.3 years ago by
svlachavas
▴ 840
21
votes
13
replies
17k
views
Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
edger
rnaseq
updated 10.5 years ago by
James W. MacDonald
68k • written 10.5 years ago by
candida.vaz
▴ 50
21
votes
1
reply
8.6k
views
Differences between limma voom E values and edgeR cpm values?
edgeR
updated 10.6 years ago by
Gordon Smyth
52k • written 10.9 years ago by
John Brothers II
▴ 90
19
votes
10
replies
8.3k
views
Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
edger
estimatedispersions
glm
updated 9.1 years ago by
Gordon Smyth
52k • written 9.1 years ago by
maltethodberg
▴ 180
19
votes
4
replies
9.2k
views
Confidence intervals on edgeR logFC
edgeR
statistics
confidence interval
updated 9.0 years ago by
nwvidal
• 0 • written 10.6 years ago by
ri.lars
▴ 40
19
votes
6
replies
35k
views
How does edgeR cpm function calculate log(CPM) values?
edgeR
cpm
updated 6.8 years ago by
ftroot1010
▴ 20 • written 7.0 years ago by
jxb.dev
▴ 40
18
votes
4
replies
37k
views
FDR and padj in deseq and edger
deseq2
edger
updated 9.5 years ago by
Gordon Smyth
52k • written 9.5 years ago by
tonja.r
▴ 80
18
votes
12
replies
4.4k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR
deseq2
rna-seq
independent filtering
updated 9.8 years ago by
Michael Love
43k • written 9.8 years ago by
Ryan C. Thompson
★ 7.9k
18
votes
17
replies
5.1k
views
How to model a comparison between comparisons in edgeR?
edger
rnaseq
updated 10.1 years ago by
Ryan C. Thompson
★ 7.9k • written 10.1 years ago by
Nick N
▴ 60
17
votes
4
replies
32k
views
RPKM, CPM and TMM
edger
rnaseq
differential expression
updated 9.8 years ago by
Aaron Lun
★ 28k • written 9.8 years ago by
Pauly Lin
▴ 160
16
votes
6
replies
3.9k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR
limma
diffSplice
DEXSeq
updated 8.7 years ago by
Charity Law
▴ 90 • written 8.7 years ago by
maltethodberg
▴ 180
16
votes
12
replies
8.6k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 7 months ago by
khanwaled68
• 0 • written 9.1 years ago by
florian.noack
▴ 60
15
votes
18
replies
4.6k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2
edgeR
goana
GO
updated 3.1 years ago by
Gordon Smyth
52k • written 3.1 years ago by
Raito92
▴ 60
15
votes
4
replies
3.4k
views
Using multiple tools for differential gene expression analysis as validation
edger
limma
deseq2
rnaseq
updated 8.8 years ago by
Ryan C. Thompson
★ 7.9k • written 8.8 years ago by
WouterDeCoster
▴ 130
13
votes
5
replies
8.6k
views
EDGE-R exact test vs QL F-test
edger
rnaseq
updated 3.0 years ago by
Sarah
• 0 • written 8.8 years ago by
kaihami
▴ 30
13
votes
11
replies
18k
views
edgeR TMM values
edger
9.3 years ago
ribioinfo
▴ 100
13
votes
3
replies
4.1k
views
EdgeR cpm: factor of 2 when adjusting library size?
edger
cpm
9.3 years ago
mikaelhc
▴ 20
13
votes
20
replies
15k
views
Can I feed TCGA normalized count data to EdgeR for differential gene expression analysis
EdgeR
TCGA
normalized count
updated 10.1 years ago by
alakatos
▴ 130 • written 10.1 years ago by
ycding
▴ 10
13
votes
10
replies
4.5k
views
Big differences in logfoldchange for some genes between edgeR and DESeq2
edger
deseq2
updated 9.4 years ago by
Gordon Smyth
52k • written 9.4 years ago by
Matarit
• 0
13
votes
16
replies
6.0k
views
Using edgeR or DESeq2 to analyze allele-specific expression?
edgeR
deseq2
ase
allele
9.5 years ago
trianglescout
▴ 40
13
votes
11
replies
13k
views
RNA-Seq, generate batch-free count matrix
edgeR
sva
updated 10.5 years ago by
Gordon Smyth
52k • written 10.8 years ago by
Brian Haas
▴ 90
12
votes
6
replies
3.9k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq
deseq2
edger
9.4 years ago
martiningi
▴ 40
12
votes
10
replies
7.5k
views
edgeR glmLRT with test="F"?
edger
dge
differential expression
updated 9.9 years ago by
Aaron Lun
★ 28k • written 9.9 years ago by
Ryan C. Thompson
★ 7.9k
12
votes
2
replies
4.0k
views
How does edgeR compare to lme4?
rna-seq
edger
mixed model
random effects
lme4
updated 8.8 years ago by
Gordon Smyth
52k • written 8.8 years ago by
Ekarl2
▴ 80
12
votes
4
replies
5.0k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 6.3 years ago by
Gordon Smyth
52k • written 7.9 years ago by
wd
▴ 30
12
votes
12
replies
2.9k
views
FDR does not change between genes in edgeR
RNAseq
edgeR
updated 6.3 years ago by
Gordon Smyth
52k • written 6.3 years ago by
apfelbapfel
▴ 30
12
votes
13
replies
8.8k
views
EdgeR Differential Expression analysis with NAs
EdgeR
rnaseq
NA
updated 10.6 years ago by
Aaron Lun
★ 28k • written 10.6 years ago by
elliott77
• 0
12
votes
6
replies
3.1k
views
How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
edger
differential gene expression
rnaseq
updated 8.1 years ago by
Gordon Smyth
52k • written 8.1 years ago by
gabriel.rosser
▴ 20
11
votes
14
replies
4.7k
views
Setting up the Design Matrix
rnaseq
edgeR
multiple factor design
design matrix
9.3 years ago
Yogender Gowtham
▴ 20
11
votes
15
replies
3.4k
views
edgeR - MDS Plot for Count Data
edger
DEG
mds
plot
7.7 years ago • updated 7.6 years ago
baus87
• 0
11
votes
11
replies
3.9k
views
Different results in edgeR using simple vs GLM
edger
glm
rnaseq
9.5 years ago
dietahanson
▴ 30
11
votes
10
replies
11k
views
How to determine which edgeR glmFit and glmQLFit are better
edger
updated 9.3 years ago by
Gordon Smyth
52k • written 9.3 years ago by
changjiang.h.xu
▴ 10
11
votes
6
replies
2.5k
views
edger glmQLFit mix glmLRT
edger
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
Catalina Aguilar Hurtado
▴ 90
11
votes
3
replies
2.6k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
written 16 months ago by
annikagable
• 0
10
votes
14
replies
5.4k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma
edger
deseq
deseq2
updated 7.6 years ago by
Gordon Smyth
52k • written 7.6 years ago by
Nik Tuzov
▴ 90
10
votes
10
replies
7.8k
views
GLM Likelihood ratio test
rnaseq
edgeR
GLM
updated 10.2 years ago by
Gordon Smyth
52k • written 10.2 years ago by
ygowtha
• 0
10
votes
9
replies
4.2k
views
EdgeR Multifactorial design with batch effect-trouble with defining contrasts
edger
design and contrast matrix
multiple factor design
multiple comparisons
updated 9.8 years ago by
James W. MacDonald
68k • written 9.8 years ago by
mouchkam
▴ 20
10
votes
10
replies
2.2k
views
RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
limma
edger
updated 4.6 years ago by
James W. MacDonald
68k • written 4.6 years ago by
astigliani31
▴ 10
10
votes
6
replies
5.3k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq
deseq2
edger
voom
limma
updated 7.6 years ago by
Paul Harrison
▴ 100 • written 9.9 years ago by
Sean Davis
21k
9
votes
11
replies
11k
views
Filtering of RNA-seq data in EdgeR
rnaseq
edger
filtering
updated 8.8 years ago by
David ROUX
▴ 20 • written 8.9 years ago by
alireza_sharifian_10
▴ 20
9
votes
6
replies
2.3k
views
Representative gene expression value in one condition with several replicates
rnaseq
gene expression
edger
updated 7.3 years ago by
Gordon Smyth
52k • written 7.3 years ago by
Jack
▴ 20
9
votes
16
replies
8.4k
views
edger, trended or common dispersion
edger
updated 8.8 years ago by
David ROUX
▴ 20 • written 9.4 years ago by
tonja.r
▴ 80
9
votes
7
replies
3.6k
views
How to use normalized values by EDASeq in edgeR?
edgeR
EDASeq
updated 9.7 years ago by
Gordon Smyth
52k • written 9.7 years ago by
rahilsethi
• 0
9
votes
7
replies
2.1k
views
EdgeR returns small logFC values when using GLM approach
edger
glm
logfc
9.0 years ago
gergely.zsuzsa.n
• 0
9
votes
8
replies
7.1k
views
sva + egdeR - differential expression analysis - RNA-seq data
sva
edgeR
9.3 years ago
mrodrigues.fernanda
▴ 10
9
votes
9
replies
2.9k
views
edgeR: Tagwise dispersion when using offset matrix
edger
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 years ago by
my4
▴ 10
9
votes
3
replies
8.7k
views
Doubt about the "zero expression" genes or genes with no reads at all in the count matrix file
EDGER
10.3 years ago
candida.vaz
▴ 50
9
votes
5
replies
6.0k
views
Differential expression analysis: Permutation Test
deseq2
limma
edger
permutation
updated 17 months ago by
Gordon Smyth
52k • written 9.2 years ago by
Radek
▴ 90
50 results • Page
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Comment: DeSeq Strategies for run to run Replication
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43k
You shouldn't need to run `DESeq` on the test data, or manually compute normalization factors. ``` dds_test <- ... # create object dds_te…
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Votes
Comment: Differential expression analysis using two TCGA datasets
C: Annotating HTA 2.0 genes
C: Annotating HTA 2.0 genes
A: Annotating HTA 2.0 genes
A: Annotating HTA 2.0 genes
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