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 :
batch
•
reset
0
votes
4
replies
2.5k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
7.4 years ago
j.viana
• 0
3
votes
3
replies
907
views
Correcting the batch effect in Edgeseq data
DESeq2
Edgeseq
batch
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
AZ
▴ 30
0
votes
3
replies
924
views
DESEQ2 Batch effect
deseq2
batch
updated 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
sherajilir
• 0
3
votes
5
replies
1.4k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
Pietro
▴ 40
0
votes
1
reply
752
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2
batch
sva
t-test
design matrix
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
Mozart
▴ 30
10
votes
18
replies
16k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
4.8 years ago
Mozart
▴ 30
4
votes
7
replies
3.3k
views
DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2
comparison
batch
updated 3.3 years ago by
Joana.silvestre
• 0 • written 4.6 years ago by
amin.ghareyazi
• 0
6
votes
6
replies
1.5k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
english.server
▴ 20
3
votes
3
replies
959
views
DESeq2 indirect batch effect removal
deseq2
batch
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
Solarion
• 0
0
votes
1
reply
1.1k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2
ruv
batch
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
r.tom
• 0
0
votes
3
replies
921
views
Highly variable gene analysis including RUVs batch correction
deseq2
RUV
batch
highly variable genes
updated 4.1 years ago by
tmms
• 0 • written 4.1 years ago by
f_pardow
• 0
0
votes
2
replies
657
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
anshulmbi
• 0
2
votes
8
replies
4.1k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
3.6 years ago
Pietro
▴ 40
1
vote
4
replies
1.7k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA
zinbwave
batch
IntegratedData
updated 3.5 years ago by
davide risso
▴ 950 • written 3.5 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
5
replies
1.7k
views
DeSeq2 with three batches - Remove batch Effect
deseq2
batch
removebatch effect
updated 3.4 years ago by
Michael Love
41k • written 3.4 years ago by
Bine
▴ 40
0
votes
1
reply
911
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 19 months ago by
Michael Love
41k • written 19 months ago by
estafana.t98
• 0
2
votes
1
reply
1.1k
views
Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
rna-seq
edgeR
limma
removebatcheffect()
batch
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
Ekarl2
▴ 80
0
votes
2
replies
996
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch
RNASeq
BatchEffect
DESeq2
updated 2.2 years ago by
Steve Lianoglou
★ 13k • written 2.2 years ago by
Jonas
• 0
1
vote
7
replies
1.2k
views
Comparison DESeq results using different model
Batch
BatchEffect
DESeq2
updated 2.1 years ago by
James W. MacDonald
65k • written 2.1 years ago by
dequattro.concetta
▴ 10
4
votes
1
reply
1.1k
views
on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 14 months ago by
ATpoint
★ 4.0k • written 14 months ago by
luca.s
▴ 50
0
votes
1
reply
906
views
Limma: Correct for location and batch effect
limma
BatchEffect
duplicatecorrelation
block
batch
updated 3.3 years ago by
Kevin Blighe
★ 3.9k • written 3.3 years ago by
Katherine
• 0
21 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
transcript name mapping between human and mouse
transcript name mapping between human and mouse
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
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
France,
22 minutes ago
France,
28 minutes ago
Italy,
48 minutes ago
France,
52 minutes ago
Türkiye,
1 hour ago
Traffic: 819 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