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 :
removeBatchEffect
•
reset
2
votes
2
replies
348
views
Batch adjustment for cohort based RNA seq data
RNASeqPower
removeBatchEffect
cpm
Batcheffect
12 weeks ago
sukeshinik5
▴ 20
17
votes
9
replies
7.1k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 3 months ago by
James W. MacDonald
67k • written 8.6 years ago by
ompandey
▴ 10
4
votes
4
replies
1.2k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma
adjustment
voom
removeBatchEffect
covariates
6 months ago • updated 5 months ago
sukeshinik5
▴ 20
0
votes
2
replies
1.3k
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
23 months ago
dqt
• 0
0
votes
5
replies
4.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.9 years ago by
ATpoint
★ 4.6k • written 3.7 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
970
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect
limma
updated 4.8 years ago by
Gordon Smyth
52k • written 4.8 years ago by
Sam
▴ 10
5
votes
7
replies
3.1k
views
logCPM to CPM conversion after removeBatchEffect()
edger
removeBatchEffect
cpm
logCPM
limma
5.6 years ago
altintas.ali
• 0
1
vote
6
replies
2.0k
views
edgeR removing batch effect before using expression data for clustering
edger
r
batcheffect
clustering
removeBatchEffect
updated 5.6 years ago by
James W. MacDonald
67k • written 5.6 years ago by
Biologist
▴ 120
2
votes
5
replies
4.6k
views
Batch Effect Correction
batch effect
removebatcheffect
edgeR
rld
DEseq2
6.4 years ago
Antonio Ahn
▴ 10
1
vote
1
reply
1.8k
views
Batch effect removal before SC3?
SC3
batch effect
removebatcheffect
updated 7.0 years ago by
Vladimir Kiselev
▴ 150 • written 7.0 years ago by
muad.abdelhay
▴ 10
11
votes
8
replies
12k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 7.3 years ago by
Gordon Smyth
52k • written 7.3 years ago by
lirongrossmann
▴ 80
9
votes
8
replies
9.9k
views
removeBatchEffect options: design and covariates
limma
removebatcheffect
updated 7.3 years ago by
Gordon Smyth
52k • written 10.4 years ago by
Rao,Xiayu
▴ 550
0
votes
1
reply
2.7k
views
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva
R
removebatcheffect
7.6 years ago
aina.jene
▴ 10
2
votes
2
replies
2.3k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva
removebatcheffect
R
updated 7.6 years ago by
sina.nassiri
▴ 130 • written 7.6 years ago by
aina.jene
▴ 10
1
vote
3
replies
1.5k
views
Re-use limma beta coefficients
limma
removebatcheffect
8.1 years ago
Keifa
▴ 10
3
votes
6
replies
2.8k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 8.2 years ago by
Jakub
▴ 50 • written 8.2 years ago by
amoltej
▴ 10
0
votes
3
replies
1.6k
views
How to remove nested batch effects with removeBatchEffect?
edgeR
removeBatchEffect
nested design
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
Jenny Drnevich
★ 2.0k
4
votes
5
replies
2.9k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq
edger
ruvg
removebatcheffect
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
g.atla
▴ 10
9
votes
10
replies
14k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma
removeBatchEffect
heatmap
clustering
updated 8.9 years ago by
Bernd Klaus
▴ 610 • written 8.9 years ago by
Ekarl2
▴ 80
19 results • Page
1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
xiaofeiwang198266
• 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
Awards
• All
Popular Question
to
Ali Barry
▴ 40
Popular Question
to
gabriel.hoffman
▴ 170
Popular Question
to
Jenny Drnevich
★ 2.0k
Popular Question
to
martin.grigorov
▴ 10
Scholar
to
James W. MacDonald
67k
Locations
• All
United States,
1 minute ago
France,
32 minutes ago
United Kingdom,
1 hour ago
WEHI, Melbourne, Australia,
4 hours ago
30 N Gould St STE 39034 Sheridan, WY,
4 hours ago
Traffic: 558 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