R: Normalization

normalize {RPPASPACE}

R Documentation

Normalization

Description

This function performs normalization for sample loading after quantification. It is typically invoked as part of the process of creating summary information from an RPPASet object.

Usage

## S4 method for signature 'MatrixLike'
normalize(object,
          method=getRegisteredNormalizationMethodKeys(),
          calc.medians=TRUE,
          sweep.cols=calc.medians,
          ...)

Arguments

`object`	data frame or matrix to be normalized
`method`	character string specifying name of method of sample loading normalization (see section ‘Details’ below)
`calc.medians`	logical scalar. If `TRUE`, calculate row and column median values from the data to be normalized.
`sweep.cols`	logical scalar. If `TRUE`, subtract column medians from data values prior to invoking the normalization method.
`...`	extra arguments for normalization routines

Details

By default, column medians are subtracted from the input data values; these adjusted data values are then passed to the requested normalization routine for further processing.

The method argument may be augmented with user-provided normalization methods. Package-provided values are:

medpolish	Tukey's median polish normalization
median	sample median normalization
house	housekeeping normalization
vs	variable slope normalization
none	no normalization done

Specifying “median” as the method argument causes the row median to be subtracted from each sample. Specifying “house” causes the median of one or more housekeeping antibodies to be used. The names of the antibodies to be used must be supplied as a named argument to this method. Specifying “vs” causes the sample median to be used along with a multiplicative gamma (see reference below).

Value

Returns normalized concentrations as matrix appropriately annotated.

Author(s)

P. Roebuck paul_roebuck@comcast.net, E. Shannon Neeley sneeley@stat.byu.edu, James M. Melott jmmelott@mdanderson.org