affycomp (version 1.48.0)

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.