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COMBAT
•
reset
0
votes
4
replies
710
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
5 months ago
Lucy
▴ 60
5
votes
2
replies
1.4k
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
11 months ago
Federico
▴ 10
0
votes
0
replies
589
views
combat for batch effect correction in EPIC array data
Epigenetics
combat
EPIC
18 months ago
Jitendra
▴ 10
1
vote
2
replies
1.9k
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
2.3 years ago
takemoto
• 0
0
votes
1
reply
1.2k
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 2.4 years ago by
Gordon Smyth
51k • written 2.4 years ago by
Mageiros
• 0
1
vote
4
replies
6.7k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
3.0 years ago
NewBioInfo
▴ 10
5
votes
8
replies
2.9k
views
Combat and dds Object
DESeq2
combat
updated 19 months ago by
ATpoint
★ 4.4k • written 3.1 years ago by
Bine
▴ 50
0
votes
0
replies
815
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix
comBat
3.5 years ago
joannew
• 0
1
vote
4
replies
2.4k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 11 months ago by
Hamza
• 0 • written 3.5 years ago by
zeegzaag
• 0
1
vote
8
replies
1.6k
views
Error in running Combat function
sva
ComBat
updated 3.7 years ago by
Kevin Blighe
★ 4.0k • written 3.7 years ago by
Reza
▴ 10
0
votes
5
replies
1.2k
views
Variable of interest in combat correction
sva
combat
updated 3.9 years ago by
James W. MacDonald
67k • written 3.9 years ago by
ch_el
▴ 10
0
votes
3
replies
1.2k
views
Extracting a subset of samples following SVA
Combat
SVA
Limma
updated 4.0 years ago by
Kevin Blighe
★ 4.0k • written 4.0 years ago by
jonellevillar
• 0
7
votes
6
replies
2.0k
views
sva ComBat implementation for multiple sources of batch effects
sva
combat
batch-adjustment
updated 4.4 years ago by
W. Evan Johnson
▴ 850 • written 4.4 years ago by
Zach Roe
▴ 10
1
vote
2
replies
1.1k
views
Validity of duplicateCorrelation after ComBat in this scenario
limma
ComBat
SVA
updated 4.7 years ago by
Gordon Smyth
51k • written 4.7 years ago by
vizio12341337
• 0
0
votes
0
replies
2.2k
views
adjusting for batch using ComBat (sva) - singularity error
microarray
combat
sva
batch effects
4.7 years ago
anne.bozack
• 0
0
votes
1
reply
1.0k
views
problem for interpretation of resulted ComBat() plot
ComBat
sva
batch effect
RNA-seq
updated 4.8 years ago by
W. Evan Johnson
▴ 850 • written 4.8 years ago by
modarzi
▴ 10
0
votes
1
reply
1.2k
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 4.8 years ago by
Kevin Blighe
★ 4.0k • written 4.8 years ago by
lucasmiranda42
• 0
0
votes
3
replies
1.1k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 4.9 years ago by
Martin Morgan
25k • written 4.9 years ago by
dhwani2410
• 0
8
votes
18
replies
13k
views
Batch correction by using ComBat function in sva package
deseq2
combat
Knownbatcheffect
Tutorial
updated 3.6 years ago by
Samuel Daniel
• 0 • written 5.0 years ago by
rajeshparmar4
▴ 10
2
votes
2
replies
1.5k
views
Modelling a multiplicative batch effect with DESeq2
deseq2
batch-effects
ComBat
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
Sam
▴ 10
2
votes
3
replies
1.2k
views
Design for introducing batch effect in DESeq2
deseq2
combat
batch effect
rna-seq
edger
updated 5.1 years ago by
swbarnes2
★ 1.4k • written 5.1 years ago by
Arindam
▴ 80
0
votes
2
replies
1.3k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2
sva
combat
updated 5.1 years ago by
Michael Love
42k • written 5.1 years ago by
ege.dedeoglu
• 0
0
votes
0
replies
893
views
The correct specification of the model matrix to ComBat
ComBat
sva
5.1 years ago
Sam
▴ 10
0
votes
6
replies
1.9k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma
deseq2
edger
scRNAseq
combat
updated 5.1 years ago by
Andrew_McDavid
▴ 270 • written 5.1 years ago by
Bogdan
▴ 670
7
votes
4
replies
4.3k
views
correcting the batch effects in Limma and SVA
limma
combat
sva
updated 5.2 years ago by
Gordon Smyth
51k • written 5.2 years ago by
Bogdan
▴ 670
4
votes
16
replies
5.4k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2
limma
combat
updated 5.3 years ago by
Michael Love
42k • written 5.3 years ago by
joseale2310
▴ 10
3
votes
12
replies
3.7k
views
ComBat normalization for batch effect change 0 values
ComBat
batch effect
sva
normalization
updated 5.4 years ago by
James W. MacDonald
67k • written 5.4 years ago by
hackingfactory
▴ 10
0
votes
0
replies
913
views
ComBat: missing peptide for one batch
batch effect
missing value
Combat
updated 6.0 years ago by
Gordon Smyth
51k • written 6.0 years ago by
hjleeab
• 0
0
votes
2
replies
1.6k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2
combat
sva
rna-seq
updated 6.0 years ago by
Michael Love
42k • written 6.0 years ago by
grimmerucsf
• 0
0
votes
0
replies
1.0k
views
ComBat covariate bias when building centroid based predictors
combat
combat sva
pamr
limma design matrix
sva
6.0 years ago
jmsendoya
• 0
0
votes
1
reply
2.0k
views
A problem in using Combat
sva
combat
updated 6.2 years ago by
W. Evan Johnson
▴ 850 • written 6.2 years ago by
linw
• 0
1
vote
9
replies
2.8k
views
Removing batch effects from microarray data based on only a subset of samples
limma
removebatcheffect()
ComBat
microarray
6.6 years ago
jaro.slamecka
▴ 140
0
votes
0
replies
1.2k
views
SVA/Combat without fitting an intercept
sva
combat
batch effect
limma
6.9 years ago
Eddie Imada
• 0
0
votes
1
reply
1.3k
views
Combat prior plots good enough?
combat
combat sva
7.0 years ago
Miss Agnieszka Aleksandra Golicz
▴ 40
2
votes
5
replies
3.1k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat
sva
updated 7.0 years ago by
W. Evan Johnson
▴ 850 • written 7.0 years ago by
JMallory
• 0
2
votes
5
replies
6.4k
views
RNA-Seq Batch correction negative values
rna-seq
batch-effect
combat
scran
sva
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
rmf
▴ 20
1
vote
1
reply
1.9k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat
microarray
batch effects
updated 7.1 years ago by
James W. MacDonald
67k • written 7.1 years ago by
DataFanatic
▴ 10
0
votes
0
replies
1.5k
views
Data format after removing batch effects using linear model vs using comBat
microarray
SVA
ComBat
Linear models
Residuals
7.1 years ago
DataFanatic
▴ 10
0
votes
4
replies
2.6k
views
DESeq2, outlier correction, Combat, NMF
deseq2
combat
outliers
NMF
updated 7.3 years ago by
Michael Love
42k • written 7.3 years ago by
noname
• 0
0
votes
0
replies
1.4k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0
limma
batch effect
affymetrix microarrays
ComBat
7.4 years ago
svlachavas
▴ 830
1
vote
1
reply
1.2k
views
How to interpret the SVA results
SVA
combat
RNA-seq
updated 7.5 years ago by
James W. MacDonald
67k • written 7.5 years ago by
xie186
• 0
10
votes
4
replies
3.2k
views
Adjust for multiple batches using combat
combat
sva
limma
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
juls
• 0
3
votes
4
replies
3.0k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 7.6 years ago by
Michael Love
42k • written 7.6 years ago by
g.atla
▴ 10
0
votes
0
replies
1.2k
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat
rnaseq
sva
7.6 years ago
Ryan C. Thompson
★ 7.9k
0
votes
6
replies
1.8k
views
Combine RNAseq datasets vst + Combat
combat
vst
deseq2
7.9 years ago
User34591
• 0
5
votes
2
replies
7.4k
views
ComBat to remove batch effects from RNA Seq data
combat
rnaseq
updated 7.9 years ago by
polemiraza
▴ 70 • written 7.9 years ago by
kerrypop
▴ 30
5
votes
3
replies
4.1k
views
about SVA: matrix of corrected expression values
SVA
COMBAT
8.0 years ago
Bogdan
▴ 670
3
votes
8
replies
2.6k
views
What type of data normalization for multiple microarrays?
normalization
microarray
combat
updated 8.0 years ago by
manimaran_1975
▴ 30 • written 8.0 years ago by
Ewelina Dratkiewicz
• 0
14
votes
2
replies
3.4k
views
voom with combat
limma
voom
combat
batch effect
updated 8.2 years ago by
Gordon Smyth
51k • written 8.2 years ago by
eldronzhou
▴ 10
0
votes
1
reply
1.4k
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray
batcheffectcorrection
affymetrix microarrays
ComBat
sva
updated 8.2 years ago by
chris86
▴ 420 • written 8.2 years ago by
svlachavas
▴ 830
50 results • Page
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Comment: Question on performing ANOVA-like analysis using limma
by
Gordon Smyth
51k
What does `sampleid` represent? If you use duplicateCorrelation(), then the blocking factor should be subject, it isn't clear from your que…
Answer: Question on performing ANOVA-like analysis using limma
by
Gordon Smyth
51k
In time course experiments such as this, it is essential to account for baseline variability between subjects, so the second analysis given…
Comment: AffylmGUI does not start wit R 4.4.1
by
Gordon Smyth
51k
Glad to hear that you have figured it out. Your experience might help other people with limmaGUI or affylmGUI on MacOS as well.
Answer: rtracklayer accessing UCSC data table not working
by
James W. MacDonald
67k
The track argument is deprecated now, so you can omit it. ``` > tbl.rmsk <- getTable(ucscTableQuery(mySession, table = "rmsk", range = …
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67k
This support site is meant to help people with specific questions about using Bioconductor software. There is a [vignette for `ROntoTools`]…
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DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Comment: Error in GOmeth function of missMethyl when EPICv2 annotation is used
Answer: unable to access Annotationhub latest record
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