Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
edgeR
•
reset
0
votes
0
replies
22
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
2 hours ago
Fabian
• 0
0
votes
1
reply
29
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
3 hours ago • updated 2 hours ago
Faisal
• 0
0
votes
1
reply
146
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
scoops_streams_06
• 0
4
votes
3
replies
417
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 1 day ago by
Gordon Smyth
50k • written 7 days ago by
Jack S.
▴ 50
2
votes
3
replies
218
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 9 days ago by
Gordon Smyth
50k • written 10 days ago by
JKim
• 0
0
votes
2
replies
212
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
z_bahari
• 0
2
votes
2
replies
198
views
between lane normalization upper quantile
EDASeq
edgeR
14 days ago • updated 10 days ago
elesofi
• 0
2
votes
2
replies
188
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
14 days ago
Sabiha
▴ 20
3
votes
4
replies
288
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 22 days ago by
Gordon Smyth
50k • written 23 days ago by
Jack S.
▴ 50
0
votes
1
reply
171
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 24 days ago by
Gordon Smyth
50k • written 25 days ago by
Fabian
• 0
0
votes
1
reply
184
views
ExactTest vs QLFTest
edgeR
updated 26 days ago by
Gordon Smyth
50k • written 29 days ago by
fr8712ca-s
• 0
0
votes
11
replies
586
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 23 days ago by
Gordon Smyth
50k • written 4 weeks ago by
mico
• 0
1
vote
6
replies
381
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
4 weeks ago
mico
• 0
5
votes
4
replies
331
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
5 weeks ago
pl23
• 0
2
votes
6
replies
335
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
5 weeks ago
tsl0026
• 0
0
votes
8
replies
525
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
6 weeks ago • updated 5 weeks ago
Marianna
▴ 10
3
votes
2
replies
306
views
How does one test for interactions in EdgeR?
edgeR
6 weeks ago
pl23
• 0
0
votes
4
replies
268
views
Nested paired design
edgeR
7 weeks ago
manduchi
▴ 10
1
vote
2
replies
238
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
7 weeks ago
mico
• 0
2
votes
3
replies
285
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
Shaimaa Gamal
• 0
0
votes
3
replies
306
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 8 weeks ago by
pl23
• 0
6
votes
7
replies
478
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
aa.machado001
• 0
1
vote
8
replies
464
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 8 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
sat
• 0
0
votes
0
replies
165
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
9 weeks ago
Jawahar
• 0
2
votes
4
replies
456
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
9 weeks ago
Sabiha
▴ 20
0
votes
3
replies
272
views
EdgeR for methylation analysis when there is no replicates
RRBSdata
edgeR
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
annasoudi
• 0
3
votes
3
replies
578
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 9 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Jurgen
• 0
4
votes
4
replies
370
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 8 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
Geo
• 0
4
votes
9
replies
1.0k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
11 weeks ago • updated 10 weeks ago
Luca
• 0
0
votes
1
reply
252
views
download problem
edgeR
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
theokirkland3
• 0
0
votes
5
replies
532
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
12 weeks ago • updated 8 weeks ago
Lucy
▴ 60
1
vote
2
replies
366
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
5
votes
2
replies
462
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
annikagable
• 0
1
vote
2
replies
321
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Jurgen
• 0
7
votes
2
replies
623
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
annikagable
• 0
0
votes
3
replies
399
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
4 months ago • updated 3 months ago
Karthik
• 0
4
votes
2
replies
522
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
alvaroperona1
▴ 10
0
votes
0
replies
236
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
5 months ago
Florian
• 0
6
votes
7
replies
851
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 5 months ago by
ATpoint
★ 4.0k • written 5 months ago by
jonas.freimuth
▴ 20
1
vote
3
replies
398
views
edgeR: Time course RNA-seq experiments
edgeR
updated 5 months ago by
ATpoint
★ 4.0k • written 5 months ago by
SuperDad
• 0
0
votes
1
reply
397
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
Giuseppe
• 0
1
vote
4
replies
652
views
MDS plot edgeR
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
jbono
▴ 10
3
votes
3
replies
533
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression
edgeR
limma
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
stuartthafass
• 0
1
vote
2
replies
665
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR
limma
6 months ago
petertam1343
• 0
1
vote
5
replies
665
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
Mohamed
▴ 30
3
votes
3
replies
501
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest
edgeR
DESeq2
6 months ago
Nisha
• 0
1
vote
5
replies
600
views
edgeR design/contrast matrix troubles
edgeR
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
alex.hart
• 0
0
votes
1
reply
459
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2
RNASeqData
edgeR
limma
DifferentialExpression
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
Sep
• 0
0
votes
0
replies
843
views
Tutorial:
Read data file containing both counts and annotation into edgeR
rpkm
edgeR
featureCounts
7 months ago • updated 6 months ago
Gordon Smyth
50k
0
votes
4
replies
795
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 7 months ago by
Michael Love
41k • written 7 months ago by
hanc
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Awards
• All
Popular Question
to
michael.s
• 0
Popular Question
to
James W. MacDonald
65k
Popular Question
to
Pierre Lindenbaum
▴ 10
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Jenny Drnevich
★ 2.0k
Locations
• All
United States,
just now
Austria,
5 minutes ago
UPF, Barcelona, Spain,
5 minutes ago
United States,
7 minutes ago
United States,
37 minutes ago
Traffic: 645 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6