Median location normalization function
This function is used for location normalization using the median of
intensity log-ratios for a group of spots. The function should be used
as an argument to the main normalization function maNormMain.
maNormMed(x=NULL, y="maM", subset=TRUE)
x |
Name of accessor method for spot statistic used to stratify the
data, usually a layout parameter, e.g. |
y |
Name of accessor method for spot statistics, usually |
subset |
A "logical" or "numeric" vector indicating the subset of points used to compute the location normalization values. |
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
subtracted from the raw log-ratios. It calls the function maMed,
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.
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.
Y. H. Yang, S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngai, and T. P. Speed (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research, Vol. 30, No. 4.
# See examples for maNormMain.
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