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 --