rmaPLM {affyPLM} | R Documentation |
This function converts an AffyBatch
into an
PLMset
by fitting a multichip model. In particular we
concentrate on the RMA model.
rmaPLM(object,normalize=TRUE,background=TRUE,background.method="RMA.2",normalize.method="quantile",background.param = list(),normalize.param=list(),output.param=list(),model.param=list())
object |
an AffyBatch |
normalize |
logical value. If TRUE normalize data using
quantile normalization |
background |
logical value. If TRUE background correct
using RMA background correction |
background.method |
name of background method to use. |
normalize.method |
name of normalization method to use. |
background.param |
A list of parameters for background routines |
normalize.param |
A list of parameters for normalization routines |
output.param |
A list of parameters controlling optional output from the routine. |
model.param |
A list of parameters controlling model procedure |
This function fits the RMA as a Probe Level Linear models to all the probesets in
an AffyBatch
.
An PLMset
Ben Bolstad bolstad@stat.berkeley.edu
Under Preparation
express
,expresso
,
rma
, threestep
# A larger example testing weight image function data(Dilution) Pset <- rmaPLM(Dilution,output.param=list(weights=TRUE)) image(Pset)