Assessment functions for Spike In Data

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Description

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

Usage

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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.

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.

Value

Lists with the necessary information to make the Figures.

Author(s)

Rafael A. Irizarry