ChuanJ/posibatch: Adjust for positional and batch effects using ComBat
posibatch allows users to adjust for positional effects and batch effects in Illumina Beadchips. Positional effects means the same sample in different physical positions on the array could be measured as different methylation or expression levels, and batch effects. Batch effects are sub-groups of measurements that have qualitatively different behaviour across conditions and are unrelated to the biological or scientific variables in a study. It uses either parametric or non-parametric empirical Bayes frameworks for adjusting data for positional effects and batch effects. Users are returned an expression or methylation matrix that has been corrected for position effects and batch effects.
Getting started
Browse package contents
Package details |
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| Author | Chuan Jiao <jiaochuan@sklmg.edu.cn>, Chao Chen <chenchao@sklmg.edu.cn>, Chunyu Liu <liucy@uic.edu> |
| Bioconductor views | BatchEffect MethylationArray Microarray MultipleComparison Normalization PositionalEffect Preprocessing RNASeq Sequencing StatisticalMethod |
| Maintainer | Chuan Jiao <jiaochuan@sklmg.edu.cn>, Chao Chen <chenchao@sklmg.edu.cn>, Chunyu Liu <liucy@uic.edu> |
| License | GPL-2 |
| Version | 1.0 |
| Package repository | View on GitHub |
| Installation |
Install the latest version of this package by entering the following in R:
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