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I just went into the duplicateCorrelation code, and I am even more confused. The code appears to set ndups=1 whenever block is not NULL, so how could I get a different answer from: corfit=duplicateCorrelation(fData[,2:7], design, ndups=2, block=c(1,1,2,2,3,3)) and corfit=duplicateCorrelation(fData[,2:7], design, ndups=1, block=c(1,1,2,2,3,3)) Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111