makeStepList {stepNorm} | R Documentation |
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.
makeStepList(A = c("median", "rlm", "loess"), PT = c("median", "rlm", "loess"), PL = c("median", "rlm", "loess"), Spatial2D = c("rlm2D", "loess2D", "aov2D", "spatialMedian"))
A |
A character string specifying the normalization models
for the adjustment of intensity or A bias:
A = NULL .
|
PT |
A character string specifying the normalization models
for the adjustment of print-tip or PT bias:
PT = NULL .
|
PL |
A character string specifying the normalization models
for the adjustment of well-plate or PL bias:
PL = NULL .
|
Spatial2D |
A character string specifying the normalization models
for the adjustment of spatial 2D bias:
Spatial2D = NULL .
|
This function provides a user friendly way to specify the parameter
wf.loc
for the main stepwise normalization function
stepWithinNorm
; see examples for details.
An object of class "list" for input to the stepWithinNorm
function.
Yuanyuan Xiao, yxiao@itsa.ucsf.edu,
Jean Yee Hwa Yang, jean@biostat.ucsf.edu
# 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)