miRcomp (version 1.2.2)

expressionComp: Compare expression estimates between two methods

Description

This function allows one to easily compare the expression estimates generated by two different algorithms. Feature / sample combinations that differ above a given threshold can be easily highlighted.

Usage

expressionComp(object1, qcThreshold1, 
                           object2, qcThreshold2, 
                           label1=NULL, label2=NULL,
                           diffThreshold=2,
                           plotType=c("scatterplot","MAplot"))

Arguments

object1

a list containing two elements: ct (the expression estimates) and qc (quality scores)

qcThreshold1

a numeric threshold corresponding to object1$qc below which values are considered low quality.

object2

a list containing two elements: ct (the expression estimates) and qc (quality scores)

qcThreshold2

a numeric threshold corresponding to object2$qc below which values are considered low quality.

label1

an optional label for plotting on the x-axis

label2

an optional label for plotting on the y-axis

diffThreshold

feature / sample combinations for which the expression estimates differ by more than this value are returned by the function and highlighted in the plot.

plotType

scatterplot or MA-plot

Value

• This function plots the expresison estimates produced by two different methods. Feature / sample combinations for which the expression estimates differ by more than diffThreshold are returned by the function and highlighted in the plot.

Examples

data(lifetech)
  data(qpcRdefault)
  tmp <- expressionComp(object1=lifetech, qcThreshold1=1.25, 
  object2=qpcRdefault,qcThreshold2=0.99,plotType="scatter")