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
4
votes
1
reply
1.2k
views
on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 15 months ago by
ATpoint
★ 4.1k • written 15 months ago by
luca.s
▴ 50
0
votes
1
reply
991
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 21 months ago by
Michael Love
42k • written 21 months ago by
estafana.t98
• 0
1
vote
7
replies
1.3k
views
Comparison DESeq results using different model
Batch
BatchEffect
DESeq2
updated 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
dequattro.concetta
▴ 10
0
votes
2
replies
1.0k
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch
RNASeq
BatchEffect
DESeq2
updated 2.4 years ago by
Steve Lianoglou
★ 13k • written 2.4 years ago by
Jonas
• 0
0
votes
1
reply
952
views
Limma: Correct for location and batch effect
limma
BatchEffect
duplicatecorrelation
block
batch
updated 3.5 years ago by
Kevin Blighe
★ 3.9k • written 3.5 years ago by
Katherine
• 0
0
votes
5
replies
1.8k
views
DeSeq2 with three batches - Remove batch Effect
deseq2
batch
removebatch effect
updated 3.6 years ago by
Michael Love
42k • written 3.6 years ago by
Bine
▴ 40
1
vote
4
replies
1.8k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA
zinbwave
batch
IntegratedData
updated 3.7 years ago by
davide risso
▴ 950 • written 3.7 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
8
replies
4.3k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
3.7 years ago
Pietro
▴ 40
0
votes
2
replies
691
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 4.1 years ago by
Michael Love
42k • written 4.1 years ago by
anshulmbi
• 0
0
votes
3
replies
971
views
Highly variable gene analysis including RUVs batch correction
deseq2
RUV
batch
highly variable genes
updated 4.2 years ago by
tmms
• 0 • written 4.2 years ago by
f_pardow
• 0
0
votes
1
reply
1.2k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2
ruv
batch
updated 4.6 years ago by
Michael Love
42k • written 4.6 years ago by
r.tom
• 0
3
votes
3
replies
985
views
DESeq2 indirect batch effect removal
deseq2
batch
updated 4.6 years ago by
Michael Love
42k • written 4.6 years ago by
Solarion
• 0
6
votes
6
replies
1.6k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
updated 4.7 years ago by
Gordon Smyth
50k • written 4.7 years ago by
english.server
▴ 20
4
votes
7
replies
3.4k
views
DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2
comparison
batch
updated 3.4 years ago by
Joana.silvestre
• 0 • written 4.7 years ago by
amin.ghareyazi
• 0
10
votes
18
replies
17k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
5.0 years ago
Mozart
▴ 30
0
votes
1
reply
776
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2
batch
sva
t-test
design matrix
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
Mozart
▴ 30
3
votes
5
replies
1.5k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
Pietro
▴ 40
0
votes
3
replies
962
views
DESEQ2 Batch effect
deseq2
batch
updated 5.2 years ago by
Michael Love
42k • written 5.2 years ago by
sherajilir
• 0
3
votes
3
replies
951
views
Correcting the batch effect in Edgeseq data
DESeq2
Edgeseq
batch
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
AZ
▴ 30
0
votes
4
replies
2.6k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
7.5 years ago
j.viana
• 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 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
Ekarl2
▴ 80
21 results • Page
1 of 1
Recent ...
Replies
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning
by
angelaesper43
• 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards
• All
Popular Question
to
Ken C
• 0
Popular Question
to
Johannes Rainer
★ 2.0k
Popular Question
to
Chris
▴ 10
Popular Question
to
Guido Hooiveld
★ 4.0k
Scholar
to
Michael Love
42k
Locations
• All
WEHI, Melbourne, Australia,
12 minutes ago
The Netherlands,
14 minutes ago
Greece,
34 minutes ago
Spain,
47 minutes ago
Spain,
50 minutes ago
Traffic: 732 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