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

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