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Showing :
ComBat
•
reset
52
votes
20
replies
43k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 7.8 years ago by
adam
• 0 • written 8.3 years ago by
AB
▴ 110
8
votes
18
replies
12k
views
Batch correction by using ComBat function in sva package
deseq2
combat
Knownbatcheffect
Tutorial
updated 3.1 years ago by
Samuel Daniel
• 0 • written 4.5 years ago by
rajeshparmar4
▴ 10
4
votes
21
replies
11k
views
DESeq2 and ComBat
deseq2
combat
updated 8.2 years ago by
Bernd Klaus
▴ 610 • written 8.2 years ago by
ribioinfo
▴ 100
7
votes
7
replies
8.2k
views
batch effect : comBat or blocking in limma ?
batch effect
combat
limma
block
updated 8.5 years ago by
Ryan C. Thompson
★ 7.9k • written 8.5 years ago by
eleonoregravier
▴ 70
5
votes
2
replies
7.1k
views
ComBat to remove batch effects from RNA Seq data
combat
rnaseq
updated 7.4 years ago by
polemiraza
▴ 70 • written 7.4 years ago by
kerrypop
▴ 30
1
vote
3
replies
6.5k
views
Combat - error - system is computationally singular
combat
software error
rnaseq
complex-design
updated 9.5 years ago by
Peter Langfelder
★ 2.9k • written 9.5 years ago by
Stefano Mangiola
▴ 10
0
votes
4
replies
6.3k
views
ComBat: Error non-conformable arguments
ComBat
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
alison.sara.waller
• 0
0
votes
6
replies
5.8k
views
ComBat with multiple batches
sva
combat
450k
8.2 years ago
ben.run974
• 0
2
votes
5
replies
5.7k
views
RNA-Seq Batch correction negative values
rna-seq
batch-effect
combat
scran
sva
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
rmf
▴ 20
1
vote
4
replies
5.6k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
2.5 years ago
NewBioInfo
▴ 10
0
votes
2
replies
5.3k
views
Combat in R (SVA package) error message
combat
software error
updated 8.9 years ago by
Peter Langfelder
★ 2.9k • written 8.9 years ago by
kimyoorin1
• 0
1
vote
1
reply
4.8k
views
Combat generating negative values, should I log2 transform first?
combat
batch effect
updated 8.5 years ago by
W. Evan Johnson
▴ 850 • written 8.5 years ago by
Ahdee
▴ 50
18
votes
18
replies
4.7k
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 8.5 years ago by
W. Evan Johnson
▴ 850 • written 8.5 years ago by
svlachavas
▴ 830
4
votes
4
replies
4.5k
views
sva::ComBat without covariate of interest?
sva
combat
updated 9.4 years ago by
W. Evan Johnson
▴ 850 • written 9.4 years ago by
Brent Pedersen
▴ 110
3
votes
4
replies
4.4k
views
Running Combat in SVA with NA values in matrix
sva
combat
8.3 years ago
CC
▴ 10
4
votes
16
replies
4.4k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2
limma
combat
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
joseale2310
▴ 10
2
votes
6
replies
3.9k
views
Combat for batch effects
combat
9.0 years ago
zhouxiuqing
• 0
10
votes
10
replies
3.9k
views
Method for batch correction
combat
sva
limma
updated 8.0 years ago by
Vegard Nygaard
▴ 110 • written 8.0 years ago by
AST
▴ 60
7
votes
4
replies
3.8k
views
correcting the batch effects in Limma and SVA
limma
combat
sva
updated 4.7 years ago by
Gordon Smyth
50k • written 4.7 years ago by
Bogdan
▴ 670
5
votes
3
replies
3.8k
views
about SVA: matrix of corrected expression values
SVA
COMBAT
7.5 years ago
Bogdan
▴ 670
2
votes
2
replies
3.5k
views
ComBat: should the variable of interest be included into model matrix
ComBat
updated 9.4 years ago by
W. Evan Johnson
▴ 850 • written 9.4 years ago by
maren.lang
▴ 10
1
vote
4
replies
3.5k
views
SVA package - for removing batch effect after DESeq - error in ComBat
sva
combat
8.7 years ago
GFM
▴ 20
0
votes
2
replies
3.4k
views
Using sva ComBat on DESeq2 Data
deseq2
DE
rnaseq
sva
combat
updated 8.2 years ago by
Michael Love
41k • written 8.2 years ago by
mbio.kyle
• 0
13
votes
2
replies
3.1k
views
voom with combat
limma
voom
combat
batch effect
updated 7.7 years ago by
Gordon Smyth
50k • written 7.7 years ago by
eldronzhou
▴ 10
3
votes
12
replies
3.1k
views
ComBat normalization for batch effect change 0 values
ComBat
batch effect
sva
normalization
updated 4.9 years ago by
James W. MacDonald
65k • written 4.9 years ago by
hackingfactory
▴ 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 7.9 years ago by
W. Evan Johnson
▴ 850 • written 7.9 years ago by
John Townsend
▴ 20
5
votes
2
replies
3.1k
views
ComBat - Including variable of interest in model matrix?
combat
sva
updated 9.4 years ago by
Jeff Leek
▴ 650 • written 9.4 years ago by
bengelmann
▴ 10
10
votes
4
replies
2.8k
views
Adjust for multiple batches using combat
combat
sva
limma
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
juls
• 0
3
votes
4
replies
2.7k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 7.1 years ago by
Michael Love
41k • written 7.1 years ago by
g.atla
▴ 10
2
votes
5
replies
2.7k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat
sva
updated 6.5 years ago by
W. Evan Johnson
▴ 850 • written 6.5 years ago by
JMallory
• 0
1
vote
1
reply
2.6k
views
sva and svaseq for unsupervised analysis of expression data
sva
combat
gene expression
batch effect
rnaseq
updated 8.5 years ago by
Jeff Leek
▴ 650 • written 8.6 years ago by
Farshad Farshidfar
▴ 10
0
votes
2
replies
2.6k
views
Remove batch effect - condition partially confounded by data
combat
differential gene expression
sva
updated 9.2 years ago by
Jeff Leek
▴ 650 • written 9.2 years ago by
AdamJ
• 0
1
vote
9
replies
2.4k
views
Removing batch effects from microarray data based on only a subset of samples
limma
removebatcheffect()
ComBat
microarray
6.2 years ago
jaro.slamecka
▴ 140
5
votes
8
replies
2.3k
views
Combat and dds Object
DESeq2
combat
updated 13 months ago by
ATpoint
★ 4.0k • written 2.7 years ago by
Bine
▴ 40
0
votes
4
replies
2.3k
views
DESeq2, outlier correction, Combat, NMF
deseq2
combat
outliers
NMF
updated 6.8 years ago by
Michael Love
41k • written 6.8 years ago by
noname
• 0
3
votes
8
replies
2.3k
views
What type of data normalization for multiple microarrays?
normalization
microarray
combat
updated 7.6 years ago by
manimaran_1975
▴ 30 • written 7.6 years ago by
Ewelina Dratkiewicz
• 0
0
votes
8
replies
2.2k
views
Combat in gene pattern error annotation
software error
ComBat
Gene Pattern
updated 6.3 years ago by
shaymaa_s_elgaafary
• 0 • written 8.7 years ago by
radhikaraheja
• 0
2
votes
7
replies
2.1k
views
ComBat Error: in solve.default(t(des) %*% des) : System is computationally singuar: ...
ComBat
sva
8.8 years ago
edammer
• 0
1
vote
1
reply
2.0k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 6.2 years ago by
Gordon Smyth
50k • written 9.0 years ago by
jaro.slamecka
▴ 140
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 8.1 years ago by
W. Evan Johnson
▴ 850 • written 8.1 years ago by
svlachavas
▴ 830
0
votes
0
replies
1.9k
views
adjusting for batch using ComBat (sva) - singularity error
microarray
combat
sva
batch effects
4.2 years ago
anne.bozack
• 0
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
8.2 years ago
svlachavas
▴ 830
1
vote
1
reply
1.8k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat
microarray
batch effects
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
DataFanatic
▴ 10
1
vote
4
replies
1.8k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 5 months ago by
Hamza
• 0 • written 3.1 years ago by
zeegzaag
• 0
0
votes
1
reply
1.7k
views
A problem in using Combat
sva
combat
updated 5.8 years ago by
W. Evan Johnson
▴ 850 • written 5.8 years ago by
linw
• 0
0
votes
6
replies
1.7k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma
deseq2
edger
scRNAseq
combat
updated 4.6 years ago by
Andrew_McDavid
▴ 270 • written 4.7 years ago by
Bogdan
▴ 670
0
votes
6
replies
1.6k
views
Combine RNAseq datasets vst + Combat
combat
vst
deseq2
7.4 years ago
User34591
• 0
1
vote
2
replies
1.6k
views
Question about the proper way to combine Illumina Human HT-12 v4 expression datasets from different labs
combat
batch effect
9.0 years ago
jaro.slamecka
▴ 140
0
votes
6
replies
1.6k
views
Problem in analysing microarray data with ComBat
combat
updated 12 months ago by
W. Evan Johnson
▴ 850 • written 8.8 years ago by
melissa.sorci
• 0
7
votes
6
replies
1.5k
views
sva ComBat implementation for multiple sources of batch effects
sva
combat
batch-adjustment
updated 3.9 years ago by
W. Evan Johnson
▴ 850 • written 3.9 years ago by
Zach Roe
▴ 10
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
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