assessSpikeIn2: New Assessment functions for Spike In Data
In affycomp: Graphics Toolbox for Assessment of Affymetrix Expression Measures

Description Usage Arguments Details Value Author(s)

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

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)

`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`.

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.

Lists with the necessary information to make the Figures.

Rafael A. Irizarry

affycomp documentation built on Nov. 8, 2020, 5:55 p.m.