Has the algorithm used by batchSOM for hexagonal topology changed in some way between R 1.9.1 and 2.0.1? In comparing between the two versions, I get identical results for rectangular topology, but very different results for hexagonal topology. (I tried to find release notes for the VR bundle that might explain the changes, but was unable to locate these anywhere.) Here's the script I use: # input data from rinput1 file rdata <- NULL rdata <- read.table("c:/temp/A8A.tmp", header=TRUE, sep=",") # keep only nonzero variance properties rdata <- rdata[, apply(rdata, 2, function(x)any(x[-1] != x[-length(x)])), drop = FALSE] # load SOM package library(class) #set seed for rng set.seed(12345) # calculate SOM gridtopo <- "hexagonal" xdim <- 5 ydim <- 5 gr <- somgrid(xdim = xdim, ydim = ydim, topo = gridtopo) rdata.som <- batchSOM(rdata, gr, c(4, 4, 2, 2, 1, 1, 1, 0, 0)) # write SOM results to stdout rdata.som # write out results write.table(rdata.som$codes, file="c:/temp/A8F.tmp", sep=",", col.names=T, row.names=F, quote=F, append = FALSE) And here are the first few lines of the (large) data file A8A.tmp: ALogP,Molecular_Weight,Num_H_Donors,Num_H_Acceptors,Num_RotatableBonds,Num_Atoms,Num_Rings,Num_AromaticRings 4.216,322.35781,0,4,6,24,2,2 5.752,429.38372,2,4,9,26,2,2 4.425,341.48871,1,5,10,22,1,1 4.366,327.46213,1,5,11,21,1,1 0.261,254.16304,0,8,5,18,2,2 6.45,316.47912,0,0,2,24,5,2 If I compare the A8F.tmp output files produced by 1.9.1 and 2.0.1, they look very different. Thanks, Dana Honeycutt