assessSpikeIn2 {affycomp}R Documentation

New Assessment functions for Spike In Data

Description

These functions are assessment functoions. Each takes an exprSet-class 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 exprSet-class containing exrpession measures for Affymetrix's spike-in experiment.
exprset An exprSet-class containing exrpession 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.

Details

assessMA2 performs the assessment for the second MA-plot (Figure 1b), assessLS performs the assessment for signal detection plot (Figure 4c), assessMA2 also perfomrs assessments used by fold-change related plots (Figures 5c-f). assessSpikeInSD is for the standard deviation assessment of Figure 2b. assessSpikeIn2 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


[Package affycomp version 1.4.3 Index]