tilingArray (version 1.50.0)

PMindex: Find the index of the exact match (PM) or background probes from a probeAnno environment

Description

Find the index of the exact match (PM) or background probes from a probeAnno environment

Usage

PMindex(probeAnno)
BGindex(probeAnno)

Arguments

probeAnno

environment with probe annotations. See package davidTiling for an example (?probeAnno).

Value

Details

These functions extract the exact match probes (PM) or background probes (from intergenic regions outside of known annotations) indices from probeAnno. These indices can be used to select the relevant rows of intensity data from the ExpressionSet object for plotting and normalization.

Examples

## library(davidTiling)
## data(davidTiling)
## data(probeAnno)
## pmind <- PMindex(probeAnno)
## mmind <- MMindex(probeAnno)
## bgind <- BGindex(probeAnno)
## boxplot(as.data.frame(log2(exprs(davidTiling))[pmind,]), outline=FALSE)