[BioC] marray: removing flagged spots from loess normalization

[Oliver R. Homann]

Hello,

I'm new to marray, and after reading all of the tutorials and playing 
around with my data, I find myself in need of a bit of advice.  I am 
attempting to load a batch of GenePix files and conduct a loess 
normalization on the unflagged spots.  I'm having no problem normalizing 
the data using the approach below, but I am unsure whether the weight 
matrix is being applied.

 > arrayTargets <- read.marrayInfo("arrayInfo.txt")
 > mraw <- read.GenePix(targets=arrayTargets)
 > normed <- maNorm(mraw, norm="loess")

After reading the documentation, it appears that I need to use the 
maNormMain function so that I can apply arguments to the maNormLoess 
function and specify my weight matrix.  However, I'm clearly running up 
against the limitations of my 'R' knowledge, as I cannot get this approach 
to work:

 > normed <- maNormMain(mraw, f.loc=list(maNormLoess(w=mraw at maW)))

If I omit the weight matrix argument it works fine, but when I use the line 
pasted above, I get the following error:

**********************************************************************************************
Error in simpleLoess(y, x, w, span, degree, parametric, drop.square, 
normalize,  :
         NA/NaN/Inf in foreign function call (arg 1)
In addition: There were 50 or more warnings (use warnings() to see the 
first 50)
 > warnings()
Warning messages:
1: at  8.2134
2: radius  7.8755
3: all data on boundary of neighborhood. make span bigger
4: at  5.3948
5: radius  29.573...
**********************************************************************************************

On a related topic, I'd also be grateful if someone could tell me the 
command required to colorize flagged spots (or omit them completely) when 
using the maPlot function.

Thanks for your time,
Oliver


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