Hi, I have a kooperberg bg subtracted object of 5 arrays that I am subsequently trying to normalize for some hybridised spike samples. The rownames of data for the spike probes (2000 of them, 37632 total probes on the array) are stored as a vector: > reserved[1:10] [1] 173 174 175 176 177 178 179 180 181 182 > KNWAspike <- normalizeWithinArrays(Kooperberg_red_green,layout,method="control",con tr olspots=reserved,iterations=10,span=1) Error in simpleLoess(y, x, w, span, degree, parametric, drop.square, normalize, : NA/NaN/Inf in foreign function call (arg 1) If I add weights=NULL to the above command, it works. Does this say there is something wrong with one/more of my data points, or are the two options (controlspots, weights) mutually exclusive? I'd kinda like to keep/use the weights. Many thanks in advance for any suggestions! Cheers, al > sessionInfo() R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" [6] "utils" "datasets" "methods" "base" other attached packages: geneplotter annotate genefilter survival Biobase "1.14.0" "1.14.1" "1.14.1" "2.32" "1.14.0" gplots gdata gtools lattice MASS "2.3.2" "2.3.1" "2.3.1" "0.15-11" "7.2-34" statmod sma limma Hmisc "1.3.0" "0.5.15" "2.10.0" "3.4-1" -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.