stepNorm (version 1.44.0)

makeStepList: 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.

Value

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

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.

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)