Compute useful summary statistics from a data object.

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Description

prepdata computes summary statistics that are useful for all platforms; prepaffy computes Affymetrix-specific ones. These are helper functions used by arrayQualityMetrics.

Usage

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prepdata(expressionset, intgroup, do.logtransform)
prepaffy(expressionset, x)

Arguments

expressionset

An object of class ExpressionSet for one colour non Affymetrix data, AffyBatch for Affymetrix data, NChannelSet for two colour arrays, or BeadLevelList for Illumina bead arrays.

intgroup, do.logtransform

as in arrayQualityMetrics.

x

A list, typically the result from a prior call to prepdata.

Details

See the vignette Working with arrayQualityMetrics report sections.

Value

A list with various derived quantities. In the case of prepaffy, the returned list is x with the additional elements appended.

Author(s)

Audrey Kauffmann, Wolfgang Huber