[BioC] error under "hclust" for expression data

Wang, Li li.wang at ttu.edu
Wed May 16 00:51:55 CEST 2012

Dear List Members

I am confronted with an error when doing hierarchical clustering for expression value clustering in R.

> d <- dist(n, method="euclidean")
Warning message:
In dist(n, method = "euclidean") : NAs introduced by coercion
> h <- hclust(d, method="ward")
Error in hclust(d, method = "ward") :
  NA/NaN/Inf in foreign function call (arg 11)

It seems that the NAs in my raw data affect it. 
I tried to remove NAs with the following two ways:
d <- na.omit(d)
d <- d[rowSums(!is.na(d))!=0, colSums(!is.na(d))!=0]

However, they didnot solve the problem.

Any comments and suggestions are very appreciated.


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