backgroundEstimate(object,method=c("minimum", "mode","intmin", "anglemode"), maxmode=3000, bincount=40, maxangle=0.3, subsample="OPA")method="mode"method="intmin" , see detailsmethod="anglemode" featureData slotSnpSetIllumina object. The Rb and Gb
matrices in the assayData slot contain estimated background values.
minimum: The allele specific minimum intensity is used.
mode: This model assumes that the first mode of the density of the
intensities is determined by the zero-allele in the data, see ref. The
signal intensity of the zero-allele should be zero, therefore this is
considered the background value.
intmin: This model assumes there is crosstalk between the alleles, and
background increases with the intensity of the other allele. The range
between 0 and the maximum of the other allele is divided in bincount
bins, and the minimum for this allele is determined for probes where the
other allele falls in a bin. A linear fit is determined though the minimum
values to obtain a gradually increasing value.
anglemode: This model finds the density modes closest to 0 and $\frac{\pi}{2}$
for polar transformed intensities, and uses this to determine background.
SnpSetIllumina-class, backgroundCorrect.SNP