Hi Guys Rather an odd title, but here goes... Basically I have read in my data in both limma (using read.maimages) and marrayInput (using read.marrayRaw). I want to normalize my data using loess normalisation, however using both packages (maNorm() and normalizeWithinArrays() methods) I get the error that I have mentioned before on this list: 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) The problem being that the whole thing bombs out and nothing has been saved, so I make no progress. NB just as an aside, using maNorm() and "echo=TRUE" I can see how far maNorm() has got before bombing out; with normalizeWithinArrays() I can't :-( I have 60 arrays in my raw data set - reading them in took a lot of time, and normalising them takes a lot of time. But basically one or more of my arrays is causing R's simpleLoess() function to bomb out, and thus I can't normalise my data. Now through a process of elimination I can probably figure out with array(s) are causing the problem, so is there a way of "removing" that array from the objects I have already created using read.maimages() and read.marrayRaw()? Or is it a case of eliminating the bad ones and then re-reading all the data in? And does anyone have any idea why I am getting the above error?? Thanks in advance for your help :-D Mick