affycomp (version 1.48.0)

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.