[BioC] Defining Weights in marrayNorm.

[Yuk Fai Leung]

Hi there, 

I have encountered the same problem of using different weights to normalize
my data recently. As a naïve biologist with limited programming skills, I
modified the maNormMain, maNormLoess and maNormMAD in a "dirty way" so that
I may use the respective weights for each array.


maNormMain <- function ( ... some codes omitted... 

    for (i in 1:ncol(maM(mbatch))) {
	globali <<- i

	... more codes omitted
}


maNormLoess <- function (x = "maA", y = "maM", z = "maPrintTip", w = NULL,
subset = TRUE, 
    span = 0.4, ...) 
{
    function(m) {
	if (is.character(z)) 
            maLoess(x = eval(call(x, m)), y = eval(call(y, m)), 
                z = eval(call(z, m)), w = w, subset = subset[,globali], 
                span = span, ...)
        else maLoess(x = eval(call(x, m)), y = eval(call(y, m)), 
            z = TRUE, w = w, subset = subset[,globali], span = span, ...)
    }
}

maNormMAD <- function (x = NULL, y = "maM", geo = TRUE, subset = TRUE) 
{
    function(m) {
	if (is.character(x)) 
            maMAD(x = eval(call(x, m)), y = eval(call(y, m)), 
                geo = geo, subset = subset[,globali])
        else maMAD(x = TRUE, y = eval(call(y, m)), geo = geo, 
            subset = subset[,globali])
    }
}

After setting these commands, I can do my normalization using those
non-control spots and weight >=0

flag <- maControls(array.raw) == "N" & maW(array.raw) >= 0
array.norm.ps <- maNormMain(array.raw, f.loc = list(maNormLoess(subset =
flag)), f.scale = list(maNormMAD(x = "maPrintTip", subset = flag)), echo =
TRUE)

Best regards,
Fai
________
Yuk Fai Leung
Bauer Center for Genomics Research
Harvard University
7 Divinity Avenue
Cambridge, MA 02138
Tel: 617-496-7134
Fax: 617-495-2196
email: yfleung at cgr.harvard.edu; yfleung at genomicshome.com
URL: http://genomicshome.com