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Showing :
ComBat
•
reset
0
votes
4
replies
390
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
23 days ago • updated 22 days ago
Lucy
▴ 60
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 3.1 years ago by
zeegzaag
• 0
5
votes
2
replies
719
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
470
views
combat for batch effect correction in EPIC array data
Epigenetics
combat
EPIC
13 months ago
Jitendra
▴ 10
0
votes
6
replies
1.6k
views
Problem in analysing microarray data with ComBat
combat
updated 13 months ago by
W. Evan Johnson
▴ 850 • written 8.9 years ago by
melissa.sorci
• 0
5
votes
8
replies
2.4k
views
Combat and dds Object
DESeq2
combat
updated 14 months ago by
ATpoint
★ 4.0k • written 2.7 years ago by
Bine
▴ 40
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
909
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 2.0 years ago by
Gordon Smyth
50k • written 2.0 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
0
votes
0
replies
684
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix
comBat
3.1 years ago
joannew
• 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
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 3.3 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
1.0k
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
921
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
960
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
879
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
984
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
2
votes
2
replies
1.3k
views
Modelling a multiplicative batch effect with DESeq2
deseq2
batch-effects
ComBat
updated 4.5 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
803
views
The correct specification of the model matrix to ComBat
ComBat
sva
4.7 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 4.7 years ago by
Andrew_McDavid
▴ 270 • written 4.7 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
4.5k
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
3.1k
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
798
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
918
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
1.8k
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
2.1k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 6.2 years ago by
Gordon Smyth
50k • written 9.1 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
2.3k
views
Combat in gene pattern error annotation
software error
ComBat
Gene Pattern
updated 6.4 years ago by
shaymaa_s_elgaafary
• 0 • written 8.7 years ago by
radhikaraheja
• 0
0
votes
0
replies
1.0k
views
SVA/Combat without fitting an intercept
sva
combat
batch effect
limma
6.5 years ago
Eddie Imada
• 0
0
votes
1
reply
1.2k
views
Combat prior plots good enough?
combat
combat sva
6.5 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 6.7 years ago by
James W. MacDonald
65k • written 6.7 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
6.7 years ago
DataFanatic
▴ 10
0
votes
4
replies
2.3k
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 7.1 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 7.2 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
7.1k
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
3.8k
views
about SVA: matrix of corrected expression values
SVA
COMBAT
7.6 years ago
Bogdan
▴ 670
50 results • Page
1 of 1
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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