withinNorm {stepNorm} | R Documentation |
This function is a wrapper function around fitWtihin
and
fit2DWithin
. It allows the user to choose from a set of
thirteen basic location normalization procedures. The function
operates on an object of class marrayRaw
or marrayNorm
and returns an object of
class Norm
.
withinNorm(marraySet, y = "maM", subset = TRUE, norm = c("none", "median", "rlm", "loess", "medianPrintTip", "rlmPrintTip", "loessPrintTip", "medianPlate", "rlmPlate", "loessPlate", "aov2D", "rlm2D", "loess2D", "spatialMedian"), ...)
marraySet |
Object of class marrayRaw or class
marrayNorm , containing intensity data for the batch of
arrays to be normalized. |
y |
Name of accessor method for spot statistics, usually the
log-ratio maM . |
subset |
A "logical" or "numeric" vector indicating the subset of points used to compute the normalization values. |
norm |
A character string specifying the normalization
procedures:
|
... |
Misc arguements for the specified norm function |
The function withinNorm
dispatches to the function
fitWithin
or fit2DWithin
with specified
arguments according to the choice of norm
. For instance,
when norm="loess"
for global intenstiy dependent robust
nonlinear normalization, withinNorm
calls
fitWithin(fun="loess")
with the default span parameter set
at 0.4. If a different span is preferred, it should be input by
span=0.2
through the argument ...
in the
withinNorm
function (see example below). For more details see
fitWithin
, fit2DWithin
and individual
fitting functions such as loessfit
.
An object of class marrayNorm
, containing
the normalized intensity data.
Yuanyuan Xiao, yxiao@itsa.ucsf.edu,
Jean Yee Hwa Yang, jean@biostat.ucsf.edu
Y. H. Yang, S. Dudoit, P. Luu, and T. P. Speed (2001). Normalization for cDNA microarray data. In M. L. Bittner, Y. Chen, A. N. Dorsel, and E. R. Dougherty (eds), Microarrays: Optical Technologies and Informatics, Vol. 4266 of Proceedings of SPIE.
D. L. Wilson, M. J. Buckley, C. A. Helliwell and I. W. Wilson (2003). New normalization methods for cDNA microarray data. Bioinformatics, Vol. 19, pp. 1325-1332.
seqWithinNorm
, stepWithinNorm
,
fitWithin
, fit2DWithin
,
loessfit
, rlmfit
.
# Examples use swirl dataset, for description type ? swirl data(swirl) # Apply loess normalization for the first slide, span=0.4 ## Not run: res.swirl1 <- withinNorm(swirl[,1], norm="loess") ## End(Not run) # Apply loess normalization for the first slide, span=0.2 ## Not run: res.swirl1 <- withinNorm(swirl[,1], norm="loess", span=0.2) ## End(Not run)