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edger
•
reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 5 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
4
votes
12
replies
3.7k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 6 months ago by
Miguel
• 0 • written 3.2 years ago by
robert.chen
• 0
0
votes
11
replies
2.7k
views
edgeR contrasts
edgeR
updated 8 months ago by
James W. MacDonald
65k • written 19 months ago by
ignadb
• 0
5
votes
11
replies
2.9k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
0
votes
11
replies
694
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 7 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
mico
• 0
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
4
votes
9
replies
1.2k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
9 months ago
Luca
• 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
3 months ago
Luca
• 0
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 8 months ago by
Novice_cam
• 0 • written 6.4 years ago by
knaxerova
▴ 10
0
votes
9
replies
837
views
estimateDisp() error
edgeR
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
ASNbioinf
• 0
2
votes
8
replies
2.2k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
12 months ago • updated 11 months ago
Luis
• 0
1
vote
8
replies
521
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 12 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
sat
• 0
0
votes
8
replies
1.3k
views
Question about filterByExpr function edgeR
edgeR
8 months ago
lucap
• 0
0
votes
8
replies
601
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
10 weeks ago • updated 9 weeks ago
Marianna
▴ 20
6
votes
7
replies
915
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
jonas.freimuth
▴ 20
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 7 months ago by
lucap
• 0 • written 3.0 years ago by
Marianna
▴ 20
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 22 months ago by
Mohamed
▴ 30
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
5
votes
7
replies
10.0k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 3 months ago by
Shaimaa Gamal
• 0 • written 7.1 years ago by
myprogramming2016
• 0
6
votes
7
replies
541
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 12 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
aa.machado001
• 0
5
votes
6
replies
391
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 10 days ago by
ATpoint
★ 4.0k • written 14 days ago by
nhaus
▴ 30
3
votes
6
replies
311
views
FilterByExpr low counts with small sample size
edgeR
6 days ago • updated 1 day ago
Jonathan
▴ 10
2
votes
6
replies
388
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
9 weeks ago
tsl0026
• 0
3
votes
6
replies
825
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
mohammedtoufiq91
▴ 10
1
vote
6
replies
447
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
8 weeks ago
mico
• 0
0
votes
6
replies
310
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 25 days ago by
Gordon Smyth
50k • written 26 days ago by
Faisal
• 0
1
vote
6
replies
2.6k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma
edger
timecourse
without replicate
voom
written 7.4 years ago by
Camila Orellana
▴ 10
9
votes
5
replies
5.0k
views
Differential expression analysis: Permutation Test
deseq2
limma
edger
permutation
updated 4 months ago by
Gordon Smyth
50k • written 8.2 years ago by
Radek
▴ 90
1
vote
5
replies
719
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
Mohamed
▴ 30
3
votes
5
replies
334
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 24 days ago by
Gordon Smyth
50k • written 26 days ago by
Fabian
• 0
1
vote
5
replies
833
views
Recommendation for large.n in filterByExpr
scRNAseq
edgeR
SingleCellExperiment
8 months ago
duez.tolga
• 0
1
vote
5
replies
656
views
edgeR design/contrast matrix troubles
edgeR
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
alex.hart
• 0
2
votes
5
replies
1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 14 months ago by
Rebekah
• 0
0
votes
5
replies
594
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
3 months ago • updated 12 weeks ago
Lucy
▴ 60
0
votes
5
replies
773
views
Model and Contrasts with 4 variables
contrast
edgeR
DESeq2
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
Cristina
• 0
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
9 months ago
mohammedtoufiq91
▴ 10
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq
edgeR
RNASeq
edgeR
updated 22 days ago by
Gordon Smyth
50k • written 11.5 years ago by
Maria Keays
▴ 30
0
votes
4
replies
321
views
Nested paired design
edgeR
10 weeks ago
manduchi
▴ 10
3
votes
4
replies
8.5k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 11 weeks ago by
Dimitris
• 0 • written 10.8 years ago by
Makis Motakis
▴ 30
0
votes
4
replies
846
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 7 months ago by
Michael Love
41k • written 8 months ago by
hanc
• 0
2
votes
4
replies
541
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
4
votes
4
replies
418
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 12 weeks ago by
James W. MacDonald
65k • written 3 months ago by
Geo
• 0
1
vote
4
replies
707
views
MDS plot edgeR
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
jbono
▴ 10
5
votes
4
replies
373
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
9 weeks ago • updated 8 weeks ago
pl23
• 0
3
votes
4
replies
697
views
Anova table edgeR limma
limma
RNASeq
edgeR
11 months ago
KATHERINE CHUERE NUNES
• 0
3
votes
4
replies
393
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Jack S.
▴ 50
0
votes
4
replies
390
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
22 days ago • updated 21 days ago
Lucy
▴ 60
0
votes
3
replies
324
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
533
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest
edgeR
DESeq2
7 months ago
Nisha
• 0
1
vote
3
replies
436
views
edgeR: Time course RNA-seq experiments
edgeR
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
SuperDad
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
by
Michael Love
41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide
by
Gordon Smyth
50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class?
by
James W. MacDonald
65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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