Dear all, I have come across a very confusing matter regarding dist() supplied by the amap package: --- m is just a test matrix > library(amap) Loading required package: mva Warning message: package 'mva' has been merged into 'stats' > m a b c aa 0.1 0.2 0.3 bb 2.0 3.0 4.0 cc 2.0 4.0 6.0 dd 0.3 0.2 0.1 > ds<-dist(m,method="pearson") > ds aa bb cc bb 7.416666e-03 cc 1.110223e-16 0.007416666 dd 2.857143e-01 0.205933333 0.2857143 > ds<-dist(m,method="correlation") > ds aa bb cc bb -4.440892e-16 cc 6.661338e-16 0 dd 2.000000e+00 2 2 > Why using method "correlation" I don't get 1-person also person corr coef is between (-1,1). Also in help it is said >>'pearson': Also named "not centered Pearson" sum(x_i y_i) /[sum(x_i^2) sum(y_i^2)]. >>'correlation': Also named "Centered Pearson" 1 - corr(x,y). Maybe corr() is not Pearson correlation ?? Or maybe the data has to be scaled? Very confusing. Maybe somebody can help me with this. Also there is a sqrt missing in the person corr coef definition. Best, Radu -- Dr. Radu Dobrin Department of Molecular Biology Princeton University Washington Road Princeton, NJ 08544-1014 Phone: 609-258-5657 E-mail: rdobrin@molbio.princeton.edu