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)