assessSD: SD Assessment functions
In affycomp: Graphics Toolbox for Assessment of Affymetrix Expression Measures

Description Usage Arguments Details Value Author(s)

Assessment function for standard deviation estimates. Takes a dilution data ExpressionSet and returns a list with necessary information to create assessment plot.

1	assessSD(exprset, method.name=NULL, logx=FALSE)

`exprset`	An `ExpressionSet` containing expression measures for Affymetrix's dilution experiment.
`method.name`	Name of expression measure being assessed.
`logx`	Logical indicating whether the average expression being computed should be logged, default no. See details.

assessSD does the assessment for Figure 7. This requires the ExpressionSet to have standard error estimates for the expression measure. Some expression measures (e.g. dChip) will have SEs in original scale, where others (e.g. RMA) will have them in log scale. For the former, use logx=TRUE.

Lists with the necessary information to make the Figures.

Rafael A. Irizarry

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