A numeric vector specifying which condition each array belongs to. E.g. if samplesets=c(2,2), then the first two replicates belong to one condition and the last two replicates belong to another condition. If NULL, each array is assumed to belong to a different condition.
genes
A numeric vector specifying which genes to analyse. If NULL, all genes are analysed.
genesToWatch
A numeric vector specifying which genes to monitor closely amongst those chosen to be analysed (see below for details).
probeAff
Stratify the mean (lambda) for the cross-hybridisation parameter (H) by categories according to probe-level sequence information.
probecat_threshold
Minimum amount of probes per probe affinity category.
rounding_dec_places
The initial probe categorisation is done by rounding affinities to the nearest rounding_dec_places decimal places. 1 is a good value.
Value
A list:
pm
Perfect Match probes.
mm
MisMatch probes.
samplesets
A numeric vector specifying which condition each array belongs to. E.g. if samplesets=c(2,2), then the first two replicates belong to one condition and the last two replicates belong to another condition. If NULL, each array is assumed to belong to a different condition.
probesets
A numeric vector specifying how probes are grouped into probesets.
numberOfCategories
Number of probe affinity categories.
categories
A numeric vector specifying which category each probe belongs to.
unknownProbeSeqs
A numeric vector specifying which probes lack sequence information.
numberOfUnknownProbeSeqs
Number of probes lacking sequence information.
genesToWatch
A numeric vector specifying which genes to monitor closely.
firstProbeInEachGeneToWatch
The starting position for each probe in each gene to monitor closely.