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 :
combat
•
reset
52
votes
20
replies
44k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 7.9 years ago by
adam
• 0 • written 8.4 years ago by
AB
▴ 110
18
votes
18
replies
4.8k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma
batch effect
ComBat
differential gene expression
updated 8.6 years ago by
W. Evan Johnson
▴ 850 • written 8.6 years ago by
svlachavas
▴ 830
13
votes
2
replies
3.1k
views
voom with combat
limma
voom
combat
batch effect
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
eldronzhou
▴ 10
10
votes
10
replies
4.0k
views
Method for batch correction
combat
sva
limma
updated 8.1 years ago by
Vegard Nygaard
▴ 110 • written 8.1 years ago by
AST
▴ 60
10
votes
4
replies
3.0k
views
Adjust for multiple batches using combat
combat
sva
limma
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
juls
• 0
8
votes
18
replies
12k
views
Batch correction by using ComBat function in sva package
deseq2
combat
Knownbatcheffect
Tutorial
updated 3.2 years ago by
Samuel Daniel
• 0 • written 4.6 years ago by
rajeshparmar4
▴ 10
7
votes
3
replies
3.1k
views
SVA: Including variable of interest in ComBat model matrix
combat sva
SVA
sva
ComBat
batch effect
updated 8.1 years ago by
W. Evan Johnson
▴ 850 • written 8.1 years ago by
John Townsend
▴ 20
7
votes
6
replies
1.7k
views
sva ComBat implementation for multiple sources of batch effects
sva
combat
batch-adjustment
updated 4.0 years ago by
W. Evan Johnson
▴ 850 • written 4.0 years ago by
Zach Roe
▴ 10
7
votes
7
replies
8.4k
views
batch effect : comBat or blocking in limma ?
batch effect
combat
limma
block
updated 8.6 years ago by
Ryan C. Thompson
★ 7.9k • written 8.6 years ago by
eleonoregravier
▴ 70
7
votes
4
replies
3.9k
views
correcting the batch effects in Limma and SVA
limma
combat
sva
updated 4.8 years ago by
Gordon Smyth
50k • written 4.8 years ago by
Bogdan
▴ 670
5
votes
8
replies
2.4k
views
Combat and dds Object
DESeq2
combat
updated 15 months ago by
ATpoint
★ 4.1k • written 2.8 years ago by
Bine
▴ 40
5
votes
3
replies
3.9k
views
about SVA: matrix of corrected expression values
SVA
COMBAT
7.6 years ago
Bogdan
▴ 670
5
votes
2
replies
7.2k
views
ComBat to remove batch effects from RNA Seq data
combat
rnaseq
updated 7.6 years ago by
polemiraza
▴ 70 • written 7.6 years ago by
kerrypop
▴ 30
5
votes
2
replies
3.1k
views
ComBat - Including variable of interest in model matrix?
combat
sva
updated 9.5 years ago by
Jeff Leek
▴ 650 • written 9.5 years ago by
bengelmann
▴ 10
5
votes
2
replies
777
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
7 months ago
Federico
▴ 10
4
votes
16
replies
4.6k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2
limma
combat
updated 4.9 years ago by
Michael Love
42k • written 4.9 years ago by
joseale2310
▴ 10
4
votes
4
replies
4.6k
views
sva::ComBat without covariate of interest?
sva
combat
updated 9.5 years ago by
W. Evan Johnson
▴ 850 • written 9.5 years ago by
Brent Pedersen
▴ 110
4
votes
21
replies
11k
views
DESeq2 and ComBat
deseq2
combat
updated 8.3 years ago by
Bernd Klaus
▴ 610 • written 8.3 years ago by
ribioinfo
▴ 100
3
votes
4
replies
4.5k
views
Running Combat in SVA with NA values in matrix
sva
combat
8.4 years ago
CC
▴ 10
3
votes
4
replies
2.8k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 7.2 years ago by
Michael Love
42k • written 7.2 years ago by
g.atla
▴ 10
3
votes
8
replies
2.4k
views
What type of data normalization for multiple microarrays?
normalization
microarray
combat
updated 7.7 years ago by
manimaran_1975
▴ 30 • written 7.7 years ago by
Ewelina Dratkiewicz
• 0
3
votes
12
replies
3.2k
views
ComBat normalization for batch effect change 0 values
ComBat
batch effect
sva
normalization
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
hackingfactory
▴ 10
2
votes
5
replies
2.8k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat
sva
updated 6.6 years ago by
W. Evan Johnson
▴ 850 • written 6.6 years ago by
JMallory
• 0
2
votes
5
replies
5.9k
views
RNA-Seq Batch correction negative values
rna-seq
batch-effect
combat
scran
sva
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
rmf
▴ 20
2
votes
6
replies
4.0k
views
Combat for batch effects
combat
9.2 years ago
zhouxiuqing
• 0
2
votes
7
replies
2.2k
views
ComBat Error: in solve.default(t(des) %*% des) : System is computationally singuar: ...
ComBat
sva
8.9 years ago
edammer
• 0
2
votes
3
replies
1.5k
views
comBat/SVA with no "variable of interest" and two batches
combat
sva
covariates
updated 8.0 years ago by
chris86
▴ 420 • written 8.0 years ago by
TP
• 0
2
votes
3
replies
1.1k
views
Design for introducing batch effect in DESeq2
deseq2
combat
batch effect
rna-seq
edger
updated 4.7 years ago by
swbarnes2
★ 1.4k • written 4.7 years ago by
ag1805x
▴ 80
2
votes
2
replies
1.3k
views
Modelling a multiplicative batch effect with DESeq2
deseq2
batch-effects
ComBat
updated 4.6 years ago by
Michael Love
42k • written 4.6 years ago by
Sam
▴ 10
2
votes
2
replies
3.6k
views
ComBat: should the variable of interest be included into model matrix
ComBat
updated 9.5 years ago by
W. Evan Johnson
▴ 850 • written 9.5 years ago by
maren.lang
▴ 10
1
vote
9
replies
2.5k
views
Removing batch effects from microarray data based on only a subset of samples
limma
removebatcheffect()
ComBat
microarray
6.3 years ago
jaro.slamecka
▴ 140
1
vote
1
reply
1.4k
views
ComBat (SVA) Application - Two Technical Effects
sva
ComBat
updated 9.3 years ago by
Bernd Klaus
▴ 610 • written 9.3 years ago by
andrew.j.skelton73
▴ 370
1
vote
2
replies
1.7k
views
Question about the proper way to combine Illumina Human HT-12 v4 expression datasets from different labs
combat
batch effect
9.2 years ago
jaro.slamecka
▴ 140
1
vote
1
reply
2.1k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 6.3 years ago by
Gordon Smyth
50k • written 9.2 years ago by
jaro.slamecka
▴ 140
1
vote
4
replies
3.5k
views
SVA package - for removing batch effect after DESeq - error in ComBat
sva
combat
8.9 years ago
GFM
▴ 20
1
vote
1
reply
2.6k
views
sva and svaseq for unsupervised analysis of expression data
sva
combat
gene expression
batch effect
rnaseq
updated 8.7 years ago by
Jeff Leek
▴ 650 • written 8.7 years ago by
Farshad Farshidfar
▴ 10
1
vote
1
reply
5.0k
views
Combat generating negative values, should I log2 transform first?
combat
batch effect
updated 8.6 years ago by
W. Evan Johnson
▴ 850 • written 8.6 years ago by
Ahdee
▴ 50
1
vote
2
replies
1.9k
views
Evaluation of diagnostic plot resulted from ComBat function regarding batch effect correction of a merged microarray dataset
ComBat
diagnostic plot
batch effect
affymetrix microarrays
sva
updated 8.3 years ago by
W. Evan Johnson
▴ 850 • written 8.3 years ago by
svlachavas
▴ 830
1
vote
1
reply
1.1k
views
How to interpret the SVA results
SVA
combat
RNA-seq
updated 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
xie186
• 0
1
vote
1
reply
1.8k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat
microarray
batch effects
updated 6.8 years ago by
James W. MacDonald
65k • written 6.8 years ago by
DataFanatic
▴ 10
1
vote
3
replies
6.6k
views
Combat - error - system is computationally singular
combat
software error
rnaseq
complex-design
updated 9.6 years ago by
Peter Langfelder
★ 3.0k • written 9.6 years ago by
Stefano Mangiola
▴ 10
1
vote
2
replies
938
views
Validity of duplicateCorrelation after ComBat in this scenario
limma
ComBat
SVA
updated 4.3 years ago by
Gordon Smyth
50k • written 4.3 years ago by
vizio12341337
• 0
1
vote
8
replies
1.4k
views
Error in running Combat function
sva
ComBat
updated 3.3 years ago by
Kevin Blighe
★ 3.9k • written 3.3 years ago by
Reza
▴ 10
1
vote
4
replies
1.9k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 6 months ago by
Hamza
• 0 • written 3.2 years ago by
zeegzaag
• 0
1
vote
4
replies
5.9k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
2.6 years ago
NewBioInfo
▴ 10
1
vote
2
replies
1.6k
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
24 months ago • updated 23 months ago
takemoto
• 0
0
votes
0
replies
1.4k
views
Data format after removing batch effects using linear model vs using comBat
microarray
SVA
ComBat
Linear models
Residuals
6.8 years ago
DataFanatic
▴ 10
0
votes
4
replies
442
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
5 weeks ago
Lucy
▴ 60
0
votes
0
replies
1.9k
views
Appropriate implementation of ComBat function for known batch effect correction and alternative methodologies of merging microarray datasets
sva
ComBat
customcdf
affymetrix microarrays
limma
8.3 years ago
svlachavas
▴ 830
0
votes
2
replies
3.4k
views
Using sva ComBat on DESeq2 Data
deseq2
DE
rnaseq
sva
combat
updated 8.3 years ago by
Michael Love
42k • written 8.3 years ago by
mbio.kyle
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: Gene set enrichment analysis
by
Guido Hooiveld
★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
Comment: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
zzrammal
• 0
thank you for your response. The problem is resolved. When i did a fit for the linear model i put NULL for the design fit <- lmFit(count_…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ziliang
• 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont
by
Denis
• 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: minfi latest update for EPIC V2 chip
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Awards
• All
Popular Question
to
Gordon Smyth
50k
Popular Question
to
maria.soler
• 0
Popular Question
to
Pietro
▴ 40
Popular Question
to
neilzhao
▴ 30
Popular Question
to
ATpoint
★ 4.1k
Locations
• All
Italy,
1 minute ago
Wageningen University, Wageningen, the Netherlands,
3 minutes ago
United States,
21 minutes ago
France,
27 minutes ago
France,
34 minutes ago
Traffic: 600 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