Hi! I am trying to use Single Channel Analysis of Two-Color Microarrays using limma. This topic is briefly discussed in limmaGui and I have some dificulties using intraspotCorrelation. Could somebody give me an example that help me to understand what is the design matrix to be used in intraspotCorrelation (the description of this matrix in the intraspotCorrelation help does not agree with the error message about the dimension of design matrix), or some reference.... Thanks in advance -- Mayte Suarez Farinas The Rockefeller University 1230 York Avenue, Box 212 New York, NY 10021 phone: 1-212-327-8186 fax: 1-212-327-7422