CODEWITHSUNDEEP
r
manjitha
manjitha

Reputation: 21

Hierarchial clustering in R

I am getting the following error when I use hclust function? How can I solve this problem? I am using windows 7 and 2.12.3 version of R.

n_seq <- 250                                                   
mat <- matrix(NA, ncol=n_seq, nrow=n_seq)    
for (idx in 1:n_seq) 
{mat[idx,idx] <- 0.0}         
for(idx in 1:(n_seq-1) )
{intemp <- read.xls("C:// clustal.xls", sheet = idx ); 
mat[(1+idx):n_seq,idx] <- intemp[1:(n_seq-idx), 11]}

fit <- hclust(as.dist(mat), method="single")

Error in hclust(as.dist(mat), method = "single") : 
NA/NaN/Inf in foreign function call (arg 11)

Please help me to solve this problem.

Upvotes: 2

Views: 5351

Answers (1)

nullglob
nullglob

Reputation: 7023

This error message arises because the distance matrix as.dist(mat) has a bad value (NA, NaN or Inf) in it. If you look in the code of hclust, the 11th argument to the foreign function call (i.e. by compiled code) is the values of the distance matrix, and this is what R is complaining about. By default, NA, NaN or Inf are not accepted by foreign function calls. See ?.Fortran for more info.

Upvotes: 4

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