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