| PMindex {tilingArray} | R Documentation |
Find the index of the exact match (PM) or background probes from a probeAnno environment
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)