preprocess {affyPLM} | R Documentation |
This function pre-processes an AffyBatch
.
preprocess(object,subset=NULL, normalize=TRUE,background=TRUE,background.method="RMA.2",normalize.method="quantile",background.param = list(),normalize.param=list(),verbosity.level=0)
object |
an AffyBatch |
subset |
a vector with the names of probesets to be used. If NULL then all probesets are used. |
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 |
list of parameters for background correction methods |
normalize.param |
list of parameters for normalization methods |
verbosity.level |
An integer specifying how much to print out. Higher values indicate more verbose. A value of 0 will print nothing |
This function carries out background correction and normalization
pre-processing steps. It does not summarize to produce gene expression
measures. All the same pre-processing methods supplied by
threestep
are supported by this function.
An AffyBatch
Ben Bolstad bmb@bmbolstad.com
Bolstad, BM (2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. PhD Dissertation. University of California, Berkeley.
if (require(affydata)) { data(Dilution) # should be equivalent to the bg and norm of rma() abatch.preprocessed <- preprocess(Dilution) }