makeStepList {stepNorm}R Documentation

Construction of a stepwise normalization list

Description

This function provides a user friendly way to construct a list for input to the function stepWithinNorm. The list indicates intended biases for correction and models for stepwise normalization.

Usage

  makeStepList(A = c("median", "rlm", "loess"), PT = c("median", "rlm",
"loess"), PL = c("median", "rlm", "loess"), Spatial2D = c("rlm2D",
"loess2D", "aov2D", "spatialMedian"))

Arguments

A A character string specifying the normalization models for the adjustment of intensity or A bias:
median:
global median location normalization
rlm:
global intensity or A-dependent robust linear normalization using the rlm function
loess:
global intensity or A-dependent robust nonlinear normalization using the loess function
The user can specify any of these three choices and the selected model will be compared based the goodness fit and model parsimony; If the correction of the $A$ bias is not desired, the user can set A = NULL.
PT A character string specifying the normalization models for the adjustment of print-tip or PT bias:
median:
within-print-tip-group median normalization
rlm:
within-print-tip-group robust linear normalization using the rlm function
loess:
within-print-tip-group robust nonlinear normalization using the loess function
none:
no normalization for the PT bias
If the correction of the $PT$ bias is not desired, the user can set PT = NULL.
PL A character string specifying the normalization models for the adjustment of well-plate or PL bias:
median:
within-well-plate median normalization
rlm:
within-well-plate robust linear normalization using the rlm function
loess:
within-well-plate robust nonlinear normalization using the loess function
none:
no normalization for the PL bias
If the correction of the $PL$ bias is not desired, the user can set PL = NULL.
Spatial2D A character string specifying the normalization models for the adjustment of spatial 2D bias:
none:
no normalization for the spatial 2D bias
aov2D:
spatial bivariate location normalization using ANOVA
rlm2D:
spatial bivariate location normalization using the rlm function
loess2D:
spatial bivariate location normalization using the loess function
spatialMedian:
spatial location normalization using a spatial median approach (see Wilson et al. (2003) in reference)
If the correction of the $PL$ bias is not desired, the user can set Spatial2D = NULL.

Details

This function provides a user friendly way to specify the parameter wf.loc for the main stepwise normalization function stepWithinNorm; see examples for details.

Value

An object of class "list" for input to the stepWithinNorm function.

Author(s)

Yuanyuan Xiao, yxiao@itsa.ucsf.edu,
Jean Yee Hwa Yang, jean@biostat.ucsf.edu

See Also

stepWithinNorm.

Examples

# Examples use swirl dataset, for description type ? swirl
data(swirl)

# To use the default parameters, which adjusts A, PT, PL and Spatial2D
# biases sequentially and compares all models available, simple type

wf.loc <- makeStepList()

# To apply loess for the A bias, and to omit the Spatial2D step
wf.loc <- makeStepList(A=("loess"), Spatial2D=NULL)

# To compare only rlm and loess in the A bias step, and other biases as default
wf.loc <- makeStepList(A=c("rlm","loess"))

# input to the stepWithinNorm function
## Not run: 
step.swirl1 <- stepWithinNorm(swirl[,1],wf.loc=wf.loc)
## End(Not run)
[Package stepNorm version 1.8.0 Index]