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AssayCorrector

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Description

This package uses partial mean polish and non-parametric statistical procedures to identify and correct spatial bias present in high-thoughput screening assays.

Installation

You can install the AssayCorrector package by typing

install.packages('devtools')
devtools::install_github('bmazoure/AssayCorrector')

If there is an error with the package mixOmics, run the following and re-try:

install.packages("https://cran.r-project.org/src/contrib/Archive/mixOmics/mixOmics_6.3.2.tar.gz", repos=NULL, type="source")

Usage

First, an assay object should be created by using

library(AssayCorrector)
# Fictive 8x12x5 assay
assay<-create_assay(m)
# Plate 7 taken from Carralot et al. 2012
assay<-create_assay(plate7)

Next, we can detect and correct the bias as follows:

detected<-detect_bias(assay,type="P",alpha=0.01)
corrected<-correct_bias(detected,method=1,type="P") # Correct the bias assuming an additive model (method=1), plate-wise only

The S3 methods print.assay() and plot.assay() override the default functions. Consult the complete pdf documentation for examples

About

The AssayCorrector eliminates spatial bias in HTS assays using PMP methods.

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