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combat
•
reset
5
votes
2
replies
624
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
6 months ago
Federico
▴ 10
0
votes
0
replies
444
views
combat for batch effect correction in EPIC array data
Epigenetics
combat
EPIC
12 months ago
Jitendra
▴ 10
1
vote
2
replies
1.5k
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
22 months ago
takemoto
• 0
0
votes
1
reply
854
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 23 months ago by
Gordon Smyth
50k • written 23 months ago by
Mageiros
• 0
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
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
0
replies
665
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix
comBat
3.0 years ago
joannew
• 0
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
1
vote
8
replies
1.4k
views
Error in running Combat function
sva
ComBat
updated 3.2 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
Reza
▴ 10
0
votes
5
replies
1.0k
views
Variable of interest in combat correction
sva
combat
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
ch_el
▴ 10
0
votes
3
replies
1.0k
views
Extracting a subset of samples following SVA
Combat
SVA
Limma
updated 3.5 years ago by
Kevin Blighe
★ 3.9k • written 3.5 years ago by
jonellevillar
• 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
1
vote
2
replies
895
views
Validity of duplicateCorrelation after ComBat in this scenario
limma
ComBat
SVA
updated 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
vizio12341337
• 0
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
1
reply
930
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 4.3 years ago by
Kevin Blighe
★ 3.9k • written 4.3 years ago by
lucasmiranda42
• 0
0
votes
1
reply
839
views
problem for interpretation of resulted ComBat() plot
ComBat
sva
batch effect
RNA-seq
updated 4.3 years ago by
W. Evan Johnson
▴ 850 • written 4.3 years ago by
modarzi
▴ 10
0
votes
3
replies
960
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 4.4 years ago by
Martin Morgan
25k • written 4.4 years ago by
dhwani2410
• 0
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
2
votes
2
replies
1.2k
views
Modelling a multiplicative batch effect with DESeq2
deseq2
batch-effects
ComBat
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
Sam
▴ 10
2
votes
3
replies
1.0k
views
Design for introducing batch effect in DESeq2
deseq2
combat
batch effect
rna-seq
edger
updated 4.6 years ago by
swbarnes2
★ 1.3k • written 4.6 years ago by
ag1805x
▴ 80
0
votes
2
replies
1.1k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2
sva
combat
updated 4.6 years ago by
Michael Love
41k • written 4.6 years ago by
ege.dedeoglu
• 0
0
votes
0
replies
780
views
The correct specification of the model matrix to ComBat
ComBat
sva
4.6 years ago
Sam
▴ 10
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
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
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
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
0
votes
0
replies
777
views
ComBat: missing peptide for one batch
batch effect
missing value
Combat
updated 5.5 years ago by
Gordon Smyth
50k • written 5.5 years ago by
hjleeab
• 0
0
votes
2
replies
1.4k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2
combat
sva
rna-seq
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
grimmerucsf
• 0
0
votes
0
replies
896
views
ComBat covariate bias when building centroid based predictors
combat
combat sva
pamr
limma design matrix
sva
5.6 years ago
jmsendoya
• 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
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
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
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
0
votes
0
replies
1.0k
views
SVA/Combat without fitting an intercept
sva
combat
batch effect
limma
6.4 years ago
Eddie Imada
• 0
0
votes
1
reply
1.1k
views
Combat prior plots good enough?
combat
combat sva
6.5 years ago
Miss Agnieszka Aleksandra Golicz
▴ 40
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
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
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
0
votes
0
replies
1.3k
views
Data format after removing batch effects using linear model vs using comBat
microarray
SVA
ComBat
Linear models
Residuals
6.7 years ago
DataFanatic
▴ 10
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
0
votes
0
replies
1.3k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0
limma
batch effect
affymetrix microarrays
ComBat
6.9 years ago
svlachavas
▴ 830
1
vote
1
reply
1.0k
views
How to interpret the SVA results
SVA
combat
RNA-seq
updated 7.0 years ago by
James W. MacDonald
65k • written 7.0 years ago by
xie186
• 0
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
2.8k
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
0
votes
0
replies
1.1k
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat
rnaseq
sva
7.1 years ago
Ryan C. Thompson
★ 7.9k
0
votes
6
replies
1.6k
views
Combine RNAseq datasets vst + Combat
combat
vst
deseq2
7.4 years ago
User34591
• 0
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
5
votes
3
replies
3.8k
views
about SVA: matrix of corrected expression values
SVA
COMBAT
7.5 years ago
Bogdan
▴ 670
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
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
50 results • Page
1 of 1
Recent ...
Replies
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
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
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
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
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