abr1: abr1 Data

In mt: Metabolomics Data Analysis Toolbox

abr1 Data

Description

An FIE-MS data.

Usage

data(abr1)

Details

abr1 is an FIE-MS data matrices developed from analysis of samples representing a time course of pathogen attack in a model plant species (Brachypodium distachyon). The data was developed in a single batch with all samples randomised using a Thermo LTQ linear ion trap. Both positive and negative ion mode are given (abr1$pos and abr1$neg).

Value

A list with the following elements:

fact	A data frame containing experimental meta-data.
pos	A data frame for positive data with 120 observations and 2000 variables.
neg	A data frame for negative data with 120 observations and 2000 variables.

Examples

# Load data set
data(abr1)

# Select data set
dat <- abr1$neg

# number of observations and variables
dim(dat)

# Transform data
dat.log   <- preproc(dat, method = "log")
dat.sqrt  <- preproc(dat, method = "sqrt")
dat.asinh <- preproc(dat, method = "asinh")

op <- par(mfrow=c(2,2), pch=16)
matplot(t(dat),main="Original",type="l",col="blue",
     ylab="Intensity")
matplot(t(dat.log),main="Log",type="l",col="green",
     ylab="Intensity")
matplot(t(dat.sqrt),main="Sqrt",type="l",col="red",
     ylab="Intensity")
matplot(t(dat.asinh),main="ArcSinh)",type="l",col="black",
     ylab="Intensity")
par(op)
mtext("Data set", line=2.5, font=3, cex=1.5)

mt documentation built on June 22, 2024, 12:24 p.m.