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ComBat specifications

Information


Unique identifier OMICS_00857
Name ComBat
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publications for ComBat

ComBat citations

 (327)
library_books

Curated compendium of human transcriptional biomarker data

2018
Sci Data
PMCID: 5903354
PMID: 29664470
DOI: 10.1038/sdata.2018.66

[…] ng effects. In the clinical annotations, we identified batch-processing information for datasets GSE25507, GSE37199, GSE39582, and GSE40292 (Data Citation 1). We corrected for batch effects using the ComBat software. The Biomarker Benchmark repository contains pre- and post-batch-corrected data. For dataset GSE37199, we identified two variables that could have been used for batch correction ("Cent […]

library_books

Epigenome wide association study of total serum immunoglobulin E in children: a life course approach

2018
Clin Epigenetics
PMCID: 5905182
PMID: 29692868
DOI: 10.1186/s13148-018-0488-x

[…] hod for background correction and dye bias adjustment [] and normalized our sample with Beta Mixture Quantile Dilation (BMIQ) []. To control for technical variability across sample plates, we applied Combat []. We report the percent of methylation for each CpG sites as β values, calculated as the signal intensity of methylated cytosines over the signal intensity of methylated and un-methylated cyt […]

library_books

Unifying cancer and normal RNA sequencing data from different sources

2018
Sci Data
PMCID: 5903355
PMID: 29664468
DOI: 10.1038/sdata.2018.61

[…] GA5. Its measurement in stomach by FeatureCounts (in default settings) is generally lower than that by RSEM (see ). In the section Technical Validation below, we primarily used results by RSEM.We ran ComBat in the R package SVAseq, to correct for non-biological variation accounting for unwanted differences between GTEx and TCGA samples of a particular tissue type. To ensure that TCGA normal sample […]

library_books

A mega analysis of expression quantitative trait loci (eQTL) provides insight into the regulatory architecture of gene expression variation in liver

2018
Sci Rep
PMCID: 5897392
PMID: 29650998
DOI: 10.1038/s41598-018-24219-z

[…] e normalize.quantiles function of the R package preprocessCore,. Since quantile normalization alone was not sufficient to normalize all studies, we adopted an empirical batch correction method called ComBat with the combat function from the sva package in R. By supplying known batch effects to the function (i.e. the study labels), ComBat standardises the data gene-wise and then applies an empirica […]

library_books

Effects of green tea on miRNA and microbiome of oral epithelium

2018
Sci Rep
PMCID: 5897334
PMID: 29651001
DOI: 10.1038/s41598-018-22994-3

[…] s. Both version V3.M and V4.M panels were used. To compensate for individual miRNA assays that were altered by the manufacturer between versions, batch effect correction was done for all assays using Combat after preliminary normalization of tests within each group. Negative controls, excluding template from the reverse transcription reaction, were tested and profiled like the samples with individ […]

call_split

Integrative multi platform meta analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers

2018
PLoS One
PMCID: 5884535
PMID: 29617451
DOI: 10.1371/journal.pone.0194844
call_split See protocol

[…] different microarray platforms to be merged by considering several batch effect removal and cross-platform correction methods. Specifically, the data were integrated using the empirical Bayes method (ComBat) []. The ComBat method merges the information from several genes with similar expression distributions in each dataset to estimate the average and variance in each of those genes []. From the i […]

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ComBat institution(s)
Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, USA

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