Dear Bioconductor list: Could anyone provide a good explanation on "duplicateCorrelaton"? There are two one-channel non-Affymetrix data sets in each of which each gene was spotted twice on each chip. To estimate correlation between duplicate values, I ran regular cor.test for each gene across all chips. The results showed average cor values as 0.52 and 0.81 for the two sets respectively. The $consensus.correlation after running "duplicateCorrelation" was shown, however, at opposite direction: 0.57 and 0.27 (even negative in some other cases). I was told once that duplicateCorrelation is the residual correlation. But I have no idea of how to coordinate two into a clear picture. We know the lower is residue the better the data are correlated (more consistent). Does this hold on residue correlation compared to total correlation as well? The on-line document on duplicateCorrelation said "consensus correlation is the trimmed mean of the individual correlations on the atanh- transformed scale". I don't know what is the atanh scale. But is it related to where I misunderstood the consensus correlation? Thanks in advance! Jianping xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Jianping Jin Ph.D. x x Bioinformatics scientist x x Center for bioinformatics x x 3133 Bioinformatics Building x x CB# 7104 x x University of North Carolina x x Chapel Hill, NC 27599 x x Tel: (919)843-6105 x x Fax: (919)843-3103 x x E-mail: jjin at email.unc.edu x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx