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.
# S4 method for MatrixLike
normalize(object,
method=getRegisteredNormalizationMethodKeys(),
calc.medians=TRUE,
sweep.cols=calc.medians,
...)Returns normalized concentrations as matrix appropriately annotated.
data frame or matrix to be normalized
character string specifying name of method of sample loading normalization (see section ‘Details’ below)
logical scalar. If TRUE, calculate row and column
median values from the data to be normalized.
logical scalar. If TRUE, subtract column medians
from data values prior to invoking the normalization method.
extra arguments for normalization routines
P. Roebuck paul_roebuck@comcast.net, E. Shannon Neeley sneeley@stat.byu.edu, James M. Melott jmmelott@mdanderson.org
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 |
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).
RPPASet