subrcModels: Fit row-column model to a matrix

In preprocessCore: A collection of pre-processing functions

Description

These functions fit row-column effect models to matrices

Usage

subrcModelPLM(y, group.labels,row.effects=NULL,input.scale=NULL)

subrcModelMedianPolish(y, group.labels)

Arguments

y	A numeric matrix
group.labels	A vector to be treated as a factor variable. This is used to assign each row to a group. NA values should be used to exclude rows from consideration

row.effects	If these are supplied then the fitting procedure uses these (and analyzes individual columns separately)
input.scale	If supplied will be used rather than estimating the scale from the data

Details

These functions fit row-column models to the specified input matrix. Specifically the model

y_ij = r_i + c_j + e_ij

with r_i and c_j as row and column effects respectively. Note that this functions treat the row effect as the parameter to be constrained using sum to zero (for rcModelPLM and rcModelWPLM) or median of zero (for rcModelMedianPolish).

The rcModelPLM and rcModelWPLM functions use a robust linear model procedure for fitting the model.

The function rcModelMedianPolish uses the median polish algorithm.

Value

A list with following items:

Estimates	The parameter estimates. Stored in column effect then row effect order
Weights	The final weights used
Residuals	The residuals
StdErrors	Standard error estimates. Stored in column effect then row effect order
Scale	Scale Estimates

Author(s)

B. M. Bolstad [e-mail]

See Also

rcModelPLM

Examples

y <- matrix(c(10+rnorm(50),20+rnorm(50)),20,5,byrow=TRUE)

subrcModelPLM(y,c(rep(1,10),rep(2,10)))
subrcModelMedianPolish(y,c(rep(1,10),rep(2,10)))



col.effects <- c(10,11,10.5,12,9.5)
row.effects <- c(seq(-0.5,-0.1,by=0.1),seq(0.1,0.5,by=0.1))


y <- outer(row.effects, col.effects,"+")
w <- runif(50)

rcModelPLM(y)
rcModelWPLM(y, w)
rcModelMedianPolish(y)

y <- y + rnorm(50)

rcModelPLM(y)
rcModelWPLM(y, w)
rcModelMedianPolish(y)



rcModelPLM(y,row.effects=row.effects)
rcModelWPLM(y,w,row.effects=row.effects)

rcModelPLM(y,input.scale=1.0)
rcModelWPLM(y, w,input.scale=1.0)
rcModelPLM(y,row.effects=row.effects,input.scale=1.0)
rcModelWPLM(y,w,row.effects=row.effects,input.scale=1.0)

preprocessCore documentation built on Jan. 10, 2021, 2:01 a.m.