Dear list, I am trying out different approaches for clustering cytometric data with R. For trying flowClust, I am using a matrix with 7 markers as columns. At the beginning I tried clustering the first two columns of the matrix (say var1 and var2) and this worked perfectly: library("flowClust") res1 <- flowClust(mydata, varNames=c("var1", "var2"), K=1, B=100) mydata2 <- mydata[mydata %in% res1,] res2 <- flowClust(mydata2, varNames=c("var1", "var2"), K=1:6, B=100) Then, I went on to trying to cluster var1 vs. var3 with the same settings, and suddenly an error occurred when calculating res2: res1 <- flowClust(mydata, varNames=c("var1", "var3"), K=1, B=100) mydata2 <- mydata[mydata %in% res1,] res2 <- flowClust(mydata2, varNames=c("var1", "var3"), K=1:6, B=100) "Error in if (M == 0) label else maxLabel[[M]] : argument has length 0" I tried to decrease the number of K, as this error did not appear when calculating res1 and it worked at up to K=1:4. Now I looked at the BIC: criterion(res2, "BIC") [1] -372.1891 -377.6957 -330.1110 NaN Where does this NaN come from? Next, I tried to add var2 as the third parameter: res1 <- flowClust(mydata, varNames=c("var1", "var2", "var3"), K=1, B=100) mydata2 <- mydata[mydata %in% res1,] res2 <- flowClust(mydata2, varNames=c("var1", "var2", "var3"), K=1:4, B=100) And again the same error as above. This time it only works with up to K=1:3, and again the third BIC is NaN. So next try: res2 <- flowClust(mydata2, varNames=c("var1", "var2", "var3"), K=1:3, B=100) # this works plot(res2[[3]], data=cmat2, level=0.8, z.cutoff=0) And here comes the next error, although it does create the plot: "Error in eigen(x@sigma[i, subset, subset]): infinite or missing values in 'x'" Adding var4 only allows K=1. I wonder what's the reason for these errors. The original data is of mode numeric, there are no NA or 0 within it. Maybe someone has an idea what I could do to eliminate this problem? I am sorry for the long email, but as I can't figure out the problem, I also can't create a short, reproducible example. All of this works fine with three columns from the rituximab data. Best wishes Anja -- Anja Mirenska Team Chipcytometry Dept. Paed. Pneumology, Allergology and Neonatology I10 E02 R7370 Hannover Medical School Carl-Neuberg-Strasse 1 30625 Hannover GERMANY phone: +49-511-5327826 web: www.chipcytometry.com [[alternative HTML version deleted]]