bg.parameters.ns {gcrma} | R Documentation |
An internal function to be used by gcrma
bg.parameters.ns(x,affinities,order.aff=NULL,Q=.25,nbreaks=40, monotonize.mu=TRUE, monotonize.sigma=FALSE)
x |
PM or MM intensities after optical background correction, before non-specific-binding correction. |
affinities |
Probe affinities for probes with known sequences. |
order.aff |
The order of affinities. If NULL , it will be
computed in this function. |
Q |
Between 0 and 1. For given affinity level, the Q-th quantile of log intensities is taken as the mean of the background distribution for this affinity level. |
nbreaks |
The number of strata of affinity levels. |
monotonize.mu |
|
monotonize.sigma |
{Logical value, if TRUE
, estimated
background standard deviation if forced to be monotonic with probe
affinity level.}
a vector of same length as x.
Rafeal Irizarry, Zhijin (Jean) Wu