affy (version 1.50.0)

assessSpikeIn: Assessment functions for Spike In Data

Description

These functions are assessment functions. Each takes an ExpressionSet and returns a list with necessary information to create assessment plots.

Usage

assessSpikeIn(s,method.name=NULL,verbose=TRUE)
assessMA(exprset,method.name=NULL)
assessSignal(exprset,method.name=NULL)
assessFC(exprset,method.name=NULL)
assessFC2(exprset,method.name=NULL)

Arguments

s

An ExpressionSet containing expression measures for Affymetrix's spike-in experiment.

exprset

An ExpressionSet containing expression measures for Affymetrix's spike-in experiment.

method.name

Name of expression measure being assessed.

verbose

logical. If TRUE show messages.

Value

• Lists with the necessary information to make the Figures.

Details

assessMA performs the assessment for the MA-plot (Figure 1), assessSignal performs the assessment for signal detection plot (Figure 4a), assessFC performs assessments used by fold-change related plots (Figures 5a, 6a, 6b). assessFC2 is for the ROC for genes with nominal fold changes of 2 (Figure 5b). assessSpikeIn is a wrapper for all these and returns a list of lists.