PMindex: Find the index of the exact match (PM) or background probes...
In tilingArray: Transcript mapping with high-density oligonucleotide tiling arrays

Description Usage Arguments Details Value Author(s) Examples

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

1 2	PMindex(probeAnno) BGindex(probeAnno)

probeAnno

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

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.

Numeric vector of indices.

Matt Ritchie <ritchie@ebi.ac.uk>

## 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)