2D spatial location normalization function
This function is used for 2D spatial location normalization, using the robust local regression function loess. It should be used as an argument to the main normalization function maNormMain.
maNorm2D(x="maSpotRow", y="maSpotCol", z="maM", g="maPrintTip", w=NULL, subset=TRUE, span=0.4, ...)
x |
Name of accessor method for spot row coordinates, usually |
y |
Name of accessor method for spot column coordinates, usually |
z |
Name of accessor method for spot statistics, usually the log-ratio |
g |
Name of accessor method for print-tip-group indices, usually |
w |
An optional numeric vector of weights. |
subset |
A "logical" or "numeric" vector indicating the subset of points used to compute the fits. |
span |
The argument |
... |
Misc arguments |
The spot statistic named in z is regressed on spot row and column coordinates, separately within print-tip-group, using the loess function.
A function with bindings for the above arguments. This latter function takes as argument an object of class "marrayRaw" (or possibly "marrayNorm"), and returns a vector of fitted values to be substracted from the raw log-ratios. It calls the function ma2D, which is not specific to microarray objects.
Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine.
S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors, The Analysis of Gene Expression Data: Methods and Software, Springer, New York.
maNormMain, ma2D, loess.
# See examples for maNormMain.
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