correction: Batch/block correction

In jasenfinch/metabolyseR: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data

Batch/block correction

Description

Correction of batch/block differences.

Usage

correctionCenter(d, block = "block", type = c("mean", "median"))

## S4 method for signature 'AnalysisData'
correctionCenter(d, block = "block", type = c("mean", "median"))

Arguments

d	S4 object of class AnalysisData
block	sample information column name to use containing sample block groupings
type	type of average to use

Details

There can sometimes be artificial batch related variability introduced into metabolomics analyses as a result of analytical instrumentation or sample preparation. With an appropriate randomised block design of sample injection order, batch related variability can be corrected using an average centring correction method of the individual features.

Value

An S4 object of class AnalysisData containing the corrected data.

Methods

• correctionCenter: Correction using group average centring.

Examples

## Initial example data preparation
library(metaboData)

d <- analysisData(abr1$neg[,200:300],abr1$fact) %>% 
 occupancyMaximum(occupancy = 2/3)
 
## Group total ion count distributions prior to correction
d %>% 
 plotTIC(by = 'day',colour = 'day')
 
## Group total ion count distributions after group median correction
d %>% 
 correctionCenter(block = 'day',type = 'median') %>% 
 plotTIC(by = 'day',colour = 'day')

jasenfinch/metabolyseR documentation built on Sept. 18, 2023, 1:25 a.m.