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COMBAT
•
reset
0
votes
4
replies
418
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
4 weeks ago
Lucy
▴ 60
5
votes
2
replies
752
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
7 months ago
Federico
▴ 10
0
votes
0
replies
483
views
combat for batch effect correction in EPIC array data
Epigenetics
combat
EPIC
13 months ago
Jitendra
▴ 10
1
vote
2
replies
1.6k
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
23 months ago
takemoto
• 0
0
votes
1
reply
935
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
Mageiros
• 0
1
vote
4
replies
5.8k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
2.6 years ago
NewBioInfo
▴ 10
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
0
votes
0
replies
696
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix
comBat
3.1 years ago
joannew
• 0
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
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
0
votes
5
replies
1.0k
views
Variable of interest in combat correction
sva
combat
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
ch_el
▴ 10
0
votes
3
replies
1.1k
views
Extracting a subset of samples following SVA
Combat
SVA
Limma
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
jonellevillar
• 0
7
votes
6
replies
1.6k
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
1
vote
2
replies
929
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
0
votes
0
replies
1.9k
views
adjusting for batch using ComBat (sva) - singularity error
microarray
combat
sva
batch effects
4.3 years ago
anne.bozack
• 0
0
votes
1
reply
975
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 4.4 years ago by
Kevin Blighe
★ 3.9k • written 4.4 years ago by
lucasmiranda42
• 0
0
votes
1
reply
894
views
problem for interpretation of resulted ComBat() plot
ComBat
sva
batch effect
RNA-seq
updated 4.4 years ago by
W. Evan Johnson
▴ 850 • written 4.4 years ago by
modarzi
▴ 10
0
votes
3
replies
995
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 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 3.2 years ago by
Samuel Daniel
• 0 • written 4.6 years ago by
rajeshparmar4
▴ 10
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
41k • written 4.6 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 4.7 years ago by
swbarnes2
★ 1.3k • written 4.7 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 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
ege.dedeoglu
• 0
0
votes
0
replies
811
views
The correct specification of the model matrix to ComBat
ComBat
sva
4.7 years ago
Sam
▴ 10
0
votes
6
replies
1.8k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma
deseq2
edger
scRNAseq
combat
updated 4.7 years ago by
Andrew_McDavid
▴ 270 • written 4.8 years ago by
Bogdan
▴ 670
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
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
41k • written 4.9 years ago by
joseale2310
▴ 10
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
0
votes
0
replies
807
views
ComBat: missing peptide for one batch
batch effect
missing value
Combat
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 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 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
grimmerucsf
• 0
0
votes
0
replies
932
views
ComBat covariate bias when building centroid based predictors
combat
combat sva
pamr
limma design matrix
sva
5.7 years ago
jmsendoya
• 0
0
votes
1
reply
1.8k
views
A problem in using Combat
sva
combat
updated 5.9 years ago by
W. Evan Johnson
▴ 850 • written 5.9 years ago by
linw
• 0
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 9.1 years ago by
jaro.slamecka
▴ 140
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
0
votes
8
replies
2.3k
views
Combat in gene pattern error annotation
software error
ComBat
Gene Pattern
updated 6.4 years ago by
shaymaa_s_elgaafary
• 0 • written 8.8 years ago by
radhikaraheja
• 0
0
votes
0
replies
1.1k
views
SVA/Combat without fitting an intercept
sva
combat
batch effect
limma
6.5 years ago
Eddie Imada
• 0
0
votes
1
reply
1.2k
views
Combat prior plots good enough?
combat
combat sva
6.6 years ago
Miss Agnieszka Aleksandra Golicz
▴ 40
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
5.8k
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
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
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
2.4k
views
DESeq2, outlier correction, Combat, NMF
deseq2
combat
outliers
NMF
updated 6.9 years ago by
Michael Love
41k • written 6.9 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
7.0 years ago
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
10
votes
4
replies
2.9k
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
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
41k • written 7.2 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
7.2 years ago
Ryan C. Thompson
★ 7.9k
0
votes
6
replies
1.7k
views
Combine RNAseq datasets vst + Combat
combat
vst
deseq2
7.5 years ago
User34591
• 0
5
votes
2
replies
7.2k
views
ComBat to remove batch effects from RNA Seq data
combat
rnaseq
updated 7.5 years ago by
polemiraza
▴ 70 • written 7.5 years ago by
kerrypop
▴ 30
5
votes
3
replies
3.9k
views
about SVA: matrix of corrected expression values
SVA
COMBAT
7.6 years ago
Bogdan
▴ 670
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
50 results • Page
1 of 1
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Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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