medianPolish: Median polish

In HenrikBengtsson/aroma.light-BioC_release: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

Description

Median polish.

Usage

## S3 method for class 'matrix'
medianPolish(X, tol=0.01, maxIter=10L, na.rm=NA, ..., .addExtra=TRUE)

Arguments

X	N-times-K matrix
tol	A numeric value greater than zero used as a threshold to identify when the algorithm has converged.
maxIter	Maximum number of iterations.
na.rm	If TRUE (FALSE), NAs are exclude (not exclude). If NA, it is assumed that X contains no NA values.
.addExtra	If TRUE, the name of argument X is returned and the returned structure is assigned a class. This will make the result compatible what medpolish returns.
...	Not used.

Details

The implementation of this method give identical estimates as medpolish, but is about 3-5 times more efficient when there are no NA values.

Value

Returns a named list structure with elements:

overall	The fitted constant term.
row	The fitted row effect.
col	The fitted column effect.
residuals	The residuals.
converged	If TRUE, the algorithm converged, otherwise not.

Author(s)

Henrik Bengtsson

See Also

medpolish.

Examples

# Deaths from sport parachuting;  from ABC of EDA, p.224:
deaths <- matrix(c(14,15,14, 7,4,7, 8,2,10, 15,9,10, 0,2,0), ncol=3, byrow=TRUE)
rownames(deaths) <- c("1-24", "25-74", "75-199", "200++", "NA")
colnames(deaths) <- 1973:1975

print(deaths)

mp <- medianPolish(deaths)
mp1 <- medpolish(deaths, trace=FALSE)
print(mp)

ff <- c("overall", "row", "col", "residuals")
stopifnot(all.equal(mp[ff], mp1[ff]))

# Validate decomposition:
stopifnot(all.equal(deaths, mp$overall+outer(mp$row,mp$col,"+")+mp$resid))

HenrikBengtsson/aroma.light-BioC_release documentation built on May 7, 2019, 1:55 a.m.