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Showing :
combat
•
reset
1
vote
2
replies
468
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
8 months ago
takemoto
• 0
0
votes
1
reply
276
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 9 months ago by
Gordon Smyth
47k • written 9 months ago by
Mageiros
• 0
1
vote
4
replies
2.5k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
16 months ago
NewBioInfo
▴ 10
4
votes
6
replies
722
views
Combat and dds Object
DESeq2
combat
updated 7 days ago by
ATpoint
★ 2.0k • written 18 months ago by
Bine
▴ 20
0
votes
0
replies
356
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix
comBat
22 months ago
joannew
• 0
1
vote
3
replies
696
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 22 months ago by
Kevin Blighe
3.7k • written 22 months ago by
zeegzaag
• 0
1
vote
8
replies
839
views
Error in running Combat function
sva
ComBat
updated 2.0 years ago by
Kevin Blighe
3.7k • written 2.0 years ago by
Reza
▴ 10
0
votes
5
replies
543
views
Variable of interest in combat correction
sva
combat
updated 2.2 years ago by
James W. MacDonald
62k • written 2.2 years ago by
ch_el
▴ 10
0
votes
3
replies
514
views
Extracting a subset of samples following SVA
Combat
SVA
Limma
updated 2.3 years ago by
Kevin Blighe
3.7k • written 2.3 years ago by
jonellevillar
• 0
7
votes
6
replies
748
views
sva ComBat implementation for multiple sources of batch effects
sva
combat
batch-adjustment
updated 2.7 years ago by
W. Evan Johnson
▴ 840 • written 2.7 years ago by
Zach Roe
▴ 10
1
vote
2
replies
491
views
Validity of duplicateCorrelation after ComBat in this scenario
limma
ComBat
SVA
updated 3.0 years ago by
Gordon Smyth
47k • written 3.0 years ago by
vizio12341337
• 0
0
votes
0
replies
1.1k
views
adjusting for batch using ComBat (sva) - singularity error
microarray
combat
sva
batch effects
3.1 years ago
anne.bozack
• 0
0
votes
1
reply
522
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 3.1 years ago by
Kevin Blighe
3.7k • written 3.1 years ago by
lucasmiranda42
• 0
0
votes
1
reply
489
views
problem for interpretation of resulted ComBat() plot
ComBat
sva
batch effect
RNA-seq
updated 3.1 years ago by
W. Evan Johnson
▴ 840 • written 3.1 years ago by
modarzi
▴ 10
0
votes
3
replies
558
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 3.2 years ago by
Martin Morgan
25k • written 3.2 years ago by
dhwani2410
• 0
8
votes
18
replies
8.2k
views
Batch correction by using ComBat function in sva package
deseq2
combat
Knownbatcheffect
Tutorial
updated 23 months ago by
Samuel Daniel
• 0 • written 3.3 years ago by
rajeshparmar4
▴ 10
2
votes
2
replies
774
views
Modelling a multiplicative batch effect with DESeq2
deseq2
batch-effects
ComBat
updated 3.3 years ago by
Michael Love
39k • written 3.3 years ago by
Sam
▴ 10
2
votes
3
replies
576
views
Design for introducing batch effect in DESeq2
deseq2
combat
batch effect
rna-seq
edger
updated 3.4 years ago by
swbarnes2
★ 1.2k • written 3.4 years ago by
ag1805x
▴ 50
0
votes
2
replies
625
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2
sva
combat
updated 3.4 years ago by
Michael Love
39k • written 3.4 years ago by
ege.dedeoglu
• 0
0
votes
0
replies
446
views
The correct specification of the model matrix to ComBat
ComBat
sva
3.5 years ago
Sam
▴ 10
0
votes
6
replies
1.2k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma
deseq2
edger
scRNAseq
combat
updated 3.5 years ago by
Andrew_McDavid
▴ 260 • written 3.5 years ago by
Bogdan
▴ 660
7
votes
4
replies
2.8k
views
correcting the batch effects in Limma and SVA
limma
combat
sva
updated 3.5 years ago by
Gordon Smyth
47k • written 3.5 years ago by
Bogdan
▴ 660
4
votes
16
replies
2.1k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2
limma
combat
updated 3.6 years ago by
Michael Love
39k • written 3.6 years ago by
joseale2310
▴ 10
3
votes
12
replies
1.9k
views
ComBat normalization for batch effect change 0 values
ComBat
batch effect
sva
normalization
updated 3.8 years ago by
James W. MacDonald
62k • written 3.8 years ago by
hackingfactory
▴ 10
0
votes
0
replies
510
views
ComBat: missing peptide for one batch
batch effect
missing value
Combat
updated 4.3 years ago by
Gordon Smyth
47k • written 4.3 years ago by
hjleeab
• 0
0
votes
2
replies
928
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2
combat
sva
rna-seq
updated 4.4 years ago by
Michael Love
39k • written 4.4 years ago by
grimmerucsf
• 0
0
votes
0
replies
564
views
ComBat covariate bias when building centroid based predictors
combat
combat sva
pamr
limma design matrix
sva
4.4 years ago
jmsendoya
• 0
0
votes
1
reply
1.2k
views
A problem in using Combat
sva
combat
updated 4.6 years ago by
W. Evan Johnson
▴ 840 • written 4.6 years ago by
linw
• 0
1
vote
1
reply
1.7k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 5.0 years ago by
Gordon Smyth
47k • written 7.9 years ago by
jaro.slamecka
▴ 130
1
vote
9
replies
1.6k
views
Removing batch effects from microarray data based on only a subset of samples
limma
removebatcheffect()
ComBat
microarray
5.0 years ago
jaro.slamecka
▴ 130
0
votes
8
replies
1.6k
views
Combat in gene pattern error annotation
software error
ComBat
Gene Pattern
updated 5.1 years ago by
shaymaa_s_elgaafary
• 0 • written 7.5 years ago by
radhikaraheja
• 0
0
votes
0
replies
688
views
SVA/Combat without fitting an intercept
sva
combat
batch effect
limma
5.3 years ago
Eddie Imada
• 0
0
votes
1
reply
723
views
Combat prior plots good enough?
combat
combat sva
5.3 years ago
Miss Agnieszka Aleksandra Golicz
▴ 40
2
votes
5
replies
1.7k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat
sva
updated 5.3 years ago by
W. Evan Johnson
▴ 840 • written 5.3 years ago by
JMallory
• 0
2
votes
5
replies
4.1k
views
RNA-Seq Batch correction negative values
rna-seq
batch-effect
combat
scran
sva
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
rmf
▴ 20
1
vote
1
reply
1.4k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat
microarray
batch effects
updated 5.5 years ago by
James W. MacDonald
62k • written 5.5 years ago by
DataFanatic
▴ 10
0
votes
0
replies
1.0k
views
Data format after removing batch effects using linear model vs using comBat
microarray
SVA
ComBat
Linear models
Residuals
5.5 years ago
DataFanatic
▴ 10
0
votes
4
replies
1.7k
views
DESeq2, outlier correction, Combat, NMF
deseq2
combat
outliers
NMF
updated 5.7 years ago by
Michael Love
39k • written 5.7 years ago by
noname
• 0
0
votes
0
replies
946
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0
limma
batch effect
affymetrix microarrays
ComBat
5.7 years ago
svlachavas
▴ 800
1
vote
1
reply
725
views
How to interpret the SVA results
SVA
combat
RNA-seq
updated 5.8 years ago by
James W. MacDonald
62k • written 5.8 years ago by
xie186
• 0
10
votes
4
replies
2.1k
views
Adjust for multiple batches using combat
combat
sva
limma
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
juls
• 0
3
votes
4
replies
2.1k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 5.9 years ago by
Michael Love
39k • written 5.9 years ago by
g.atla
▴ 10
0
votes
0
replies
803
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat
rnaseq
sva
6.0 years ago
Ryan C. Thompson
7.8k
0
votes
6
replies
1.2k
views
Combine RNAseq datasets vst + Combat
combat
vst
deseq2
6.3 years ago
User34591
• 0
5
votes
2
replies
6.3k
views
ComBat to remove batch effects from RNA Seq data
combat
rnaseq
updated 6.3 years ago by
polemiraza
▴ 70 • written 6.3 years ago by
kerrypop
▴ 30
5
votes
3
replies
3.1k
views
about SVA: matrix of corrected expression values
SVA
COMBAT
6.3 years ago
Bogdan
▴ 660
3
votes
8
replies
1.6k
views
What type of data normalization for multiple microarrays?
normalization
microarray
combat
updated 6.4 years ago by
manimaran_1975
▴ 30 • written 6.4 years ago by
Ewelina Dratkiewicz
• 0
13
votes
2
replies
2.5k
views
voom with combat
limma
voom
combat
batch effect
updated 6.5 years ago by
Gordon Smyth
47k • written 6.5 years ago by
eldronzhou
▴ 10
0
votes
1
reply
844
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray
batcheffectcorrection
affymetrix microarrays
ComBat
sva
updated 6.5 years ago by
chris86
▴ 400 • written 6.6 years ago by
svlachavas
▴ 800
50
votes
20
replies
35k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 6.7 years ago by
adam
• 0 • written 7.1 years ago by
AB
▴ 110
50 results • Page
1 of 1
Recent ...
Replies
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Bernardo
• 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report
by
Okan
• 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
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