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Showing :
ComBat
•
reset
0
votes
0
replies
103
views
combat for batch effect correction in EPIC array data
Epigenetics
combat
EPIC
11 weeks ago
Jitendra
▴ 10
1
vote
2
replies
777
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
12 months ago
takemoto
• 0
0
votes
1
reply
416
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 13 months ago by
Gordon Smyth
47k • written 13 months ago by
Mageiros
• 0
1
vote
4
replies
3.5k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
20 months ago
NewBioInfo
▴ 10
5
votes
8
replies
1.3k
views
Combat and dds Object
DESeq2
combat
updated 4 months ago by
ATpoint
★ 2.9k • written 22 months ago by
Bine
▴ 20
0
votes
0
replies
418
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix
comBat
2.2 years ago
joannew
• 0
1
vote
3
replies
938
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 2.2 years ago by
Kevin Blighe
3.8k • written 2.2 years ago by
zeegzaag
• 0
1
vote
8
replies
992
views
Error in running Combat function
sva
ComBat
updated 2.4 years ago by
Kevin Blighe
3.8k • written 2.4 years ago by
Reza
▴ 10
0
votes
5
replies
665
views
Variable of interest in combat correction
sva
combat
updated 2.6 years ago by
James W. MacDonald
63k • written 2.6 years ago by
ch_el
▴ 10
0
votes
3
replies
623
views
Extracting a subset of samples following SVA
Combat
SVA
Limma
updated 2.7 years ago by
Kevin Blighe
3.8k • written 2.7 years ago by
jonellevillar
• 0
7
votes
6
replies
984
views
sva ComBat implementation for multiple sources of batch effects
sva
combat
batch-adjustment
updated 3.1 years ago by
W. Evan Johnson
▴ 840 • written 3.1 years ago by
Zach Roe
▴ 10
1
vote
2
replies
586
views
Validity of duplicateCorrelation after ComBat in this scenario
limma
ComBat
SVA
updated 3.4 years ago by
Gordon Smyth
47k • written 3.4 years ago by
vizio12341337
• 0
0
votes
0
replies
1.3k
views
adjusting for batch using ComBat (sva) - singularity error
microarray
combat
sva
batch effects
3.4 years ago
anne.bozack
• 0
0
votes
1
reply
616
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 3.5 years ago by
Kevin Blighe
3.8k • written 3.5 years ago by
lucasmiranda42
• 0
0
votes
1
reply
581
views
problem for interpretation of resulted ComBat() plot
ComBat
sva
batch effect
RNA-seq
updated 3.5 years ago by
W. Evan Johnson
▴ 840 • written 3.5 years ago by
modarzi
▴ 10
0
votes
3
replies
667
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 3.6 years ago by
Martin Morgan
25k • written 3.6 years ago by
dhwani2410
• 0
8
votes
18
replies
9.2k
views
Batch correction by using ComBat function in sva package
deseq2
combat
Knownbatcheffect
Tutorial
updated 2.3 years ago by
Samuel Daniel
• 0 • written 3.7 years ago by
rajeshparmar4
▴ 10
2
votes
2
replies
897
views
Modelling a multiplicative batch effect with DESeq2
deseq2
batch-effects
ComBat
updated 3.7 years ago by
Michael Love
40k • written 3.7 years ago by
Sam
▴ 10
2
votes
3
replies
684
views
Design for introducing batch effect in DESeq2
deseq2
combat
batch effect
rna-seq
edger
updated 3.8 years ago by
swbarnes2
★ 1.2k • written 3.8 years ago by
ag1805x
▴ 80
0
votes
2
replies
771
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2
sva
combat
updated 3.8 years ago by
Michael Love
40k • written 3.8 years ago by
ege.dedeoglu
• 0
0
votes
0
replies
532
views
The correct specification of the model matrix to ComBat
ComBat
sva
3.8 years ago
Sam
▴ 10
0
votes
6
replies
1.3k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma
deseq2
edger
scRNAseq
combat
updated 3.8 years ago by
Andrew_McDavid
▴ 270 • written 3.8 years ago by
Bogdan
▴ 660
7
votes
4
replies
3.2k
views
correcting the batch effects in Limma and SVA
limma
combat
sva
updated 3.9 years ago by
Gordon Smyth
47k • written 3.9 years ago by
Bogdan
▴ 660
4
votes
16
replies
2.8k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2
limma
combat
updated 4.0 years ago by
Michael Love
40k • written 4.0 years ago by
joseale2310
▴ 10
3
votes
12
replies
2.2k
views
ComBat normalization for batch effect change 0 values
ComBat
batch effect
sva
normalization
updated 4.1 years ago by
James W. MacDonald
63k • written 4.1 years ago by
hackingfactory
▴ 10
0
votes
0
replies
582
views
ComBat: missing peptide for one batch
batch effect
missing value
Combat
updated 4.7 years ago by
Gordon Smyth
47k • written 4.7 years ago by
hjleeab
• 0
0
votes
2
replies
1.0k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2
combat
sva
rna-seq
updated 4.7 years ago by
Michael Love
40k • written 4.7 years ago by
grimmerucsf
• 0
0
votes
0
replies
656
views
ComBat covariate bias when building centroid based predictors
combat
combat sva
pamr
limma design matrix
sva
4.7 years ago
jmsendoya
• 0
0
votes
1
reply
1.3k
views
A problem in using Combat
sva
combat
updated 4.9 years ago by
W. Evan Johnson
▴ 840 • written 4.9 years ago by
linw
• 0
1
vote
1
reply
1.8k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 5.4 years ago by
Gordon Smyth
47k • written 8.2 years ago by
jaro.slamecka
▴ 140
1
vote
9
replies
1.8k
views
Removing batch effects from microarray data based on only a subset of samples
limma
removebatcheffect()
ComBat
microarray
5.4 years ago
jaro.slamecka
▴ 140
0
votes
8
replies
1.8k
views
Combat in gene pattern error annotation
software error
ComBat
Gene Pattern
updated 5.5 years ago by
shaymaa_s_elgaafary
• 0 • written 7.8 years ago by
radhikaraheja
• 0
0
votes
0
replies
771
views
SVA/Combat without fitting an intercept
sva
combat
batch effect
limma
5.6 years ago
Eddie Imada
• 0
0
votes
1
reply
810
views
Combat prior plots good enough?
combat
combat sva
5.7 years ago
Miss Agnieszka Aleksandra Golicz
▴ 40
2
votes
5
replies
1.9k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat
sva
updated 5.7 years ago by
W. Evan Johnson
▴ 840 • written 5.7 years ago by
JMallory
• 0
2
votes
5
replies
4.6k
views
RNA-Seq Batch correction negative values
rna-seq
batch-effect
combat
scran
sva
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
rmf
▴ 20
1
vote
1
reply
1.5k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat
microarray
batch effects
updated 5.8 years ago by
James W. MacDonald
63k • written 5.8 years ago by
DataFanatic
▴ 10
0
votes
0
replies
1.2k
views
Data format after removing batch effects using linear model vs using comBat
microarray
SVA
ComBat
Linear models
Residuals
5.8 years ago
DataFanatic
▴ 10
0
votes
4
replies
1.9k
views
DESeq2, outlier correction, Combat, NMF
deseq2
combat
outliers
NMF
updated 6.0 years ago by
Michael Love
40k • written 6.0 years ago by
noname
• 0
0
votes
0
replies
1.0k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0
limma
batch effect
affymetrix microarrays
ComBat
6.1 years ago
svlachavas
▴ 810
1
vote
1
reply
791
views
How to interpret the SVA results
SVA
combat
RNA-seq
updated 6.2 years ago by
James W. MacDonald
63k • written 6.2 years ago by
xie186
• 0
10
votes
4
replies
2.3k
views
Adjust for multiple batches using combat
combat
sva
limma
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
juls
• 0
3
votes
4
replies
2.3k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 6.3 years ago by
Michael Love
40k • written 6.3 years ago by
g.atla
▴ 10
0
votes
0
replies
885
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat
rnaseq
sva
6.3 years ago
Ryan C. Thompson
7.8k
0
votes
6
replies
1.3k
views
Combine RNAseq datasets vst + Combat
combat
vst
deseq2
6.6 years ago
User34591
• 0
5
votes
2
replies
6.6k
views
ComBat to remove batch effects from RNA Seq data
combat
rnaseq
updated 6.6 years ago by
polemiraza
▴ 70 • written 6.6 years ago by
kerrypop
▴ 30
5
votes
3
replies
3.3k
views
about SVA: matrix of corrected expression values
SVA
COMBAT
6.7 years ago
Bogdan
▴ 660
3
votes
8
replies
1.8k
views
What type of data normalization for multiple microarrays?
normalization
microarray
combat
updated 6.7 years ago by
manimaran_1975
▴ 30 • written 6.8 years ago by
Ewelina Dratkiewicz
• 0
13
votes
2
replies
2.6k
views
voom with combat
limma
voom
combat
batch effect
updated 6.9 years ago by
Gordon Smyth
47k • written 6.9 years ago by
eldronzhou
▴ 10
0
votes
1
reply
952
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray
batcheffectcorrection
affymetrix microarrays
ComBat
sva
updated 6.9 years ago by
chris86
▴ 400 • written 6.9 years ago by
svlachavas
▴ 810
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Hi Guido, Thanks for your fast reply the error was as said in my question "Annotation must be a GRanges object", when I tried to use the a…
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Hi Johannes, First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant commu…
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Did you relevel before or after calling DESeq?
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