Artificial Components for Gene Expression Data

Description

Computes the artificial components for gene expression data between two conditions for a single time point.

Usage

ac(Z, design)

ac2(Z, design)

Arguments

Details

This function computes the artificial components of Z, based on the specified design vector. First, the function scales Z so that its columns have zero mean and unit variance. Then computation of the artificial components ψ[1] and ψ[2] is performed as ψ[1] = Zv[1], where v[1] = (1, … , 1) / sqrt(p), and ψ[2] = Zv[2], where v[2] = (1, … , 1, -1, … , -1 ) / sqrt(p*p[1]*(p-p[1])). Here, p[1] is the number of treatment replicates, and v[2] has p[1] positive and p-p[1] negative entries.

Value

ac returns a matrix with the artificial components ψ[1] and ψ[2] in the columns.

ac2 returns a matrix with the second artificial component ψ[2] in the only column.

Author(s)

Juan Pablo Acosta (jpacostar@unal.edu.co).

References

Acosta, J. P. (2015) Strategy for Multivariate Identification of Differentially Expressed Genes in Microarray Data. Unpublished MS thesis. Universidad Nacional de Colombia, Bogot'a.

Examples

## Computes the artificial components for the 
## phitophthora infestans data at 60 hai.
psi <- ac(phytophthora[[4]], c(rep(1,8), rep(2,8)))
plot(x=psi[,1], y=psi[,2])

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(acde)
Loading required package: boot
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/acde/ac.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ac
> ### Title: Artificial Components for Gene Expression Data
> ### Aliases: ac ac2
> 
> ### ** Examples
> 
> ## Computes the artificial components for the 
> ## phitophthora infestans data at 60 hai.
> psi <- ac(phytophthora[[4]], c(rep(1,8), rep(2,8)))
> plot(x=psi[,1], y=psi[,2])
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>