I just used intraspotCorrelation as suggested in the online Limma documentation for single channel analysis. Over half of my estimated correlation coefficients are bigger than 1.0 in absolute value. Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111