affy (version 1.50.0)

assessSpikeIn2: New 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

assessSpikeIn2(s, method.name=NULL, verbose=TRUE)
assessSpikeInSD(exprset, method.name=NULL, span=1/3)
assessLS(exprset, method.name=NULL)
assessMA2(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.

span

span used in call to loess.

Value

• Lists with the necessary information to make the Figures.

Details

assessMA2 performs the assessment for the second MA-plot (Figure 1b), and assessLS performs the assessment for signal detection plot (Figure 4c). assessMA2 also performs assessments used by fold-change related plots (Figures 5a,b) and the ROC plots (Figures 5c,d,e). assessSpikeInSD is for the standard deviation assessment in Figure 2b. assessSpikeIn2 is a wrapper for all these and returns a list of lists.