[BioC] error under "hclust" for expression data
James F. Reid
james.reid at ifom-ieo-campus.it
Wed May 16 10:58:09 CEST 2012
check your data matrix, it looks like it might contain non-numeric data
(from the NAs introduced by coercion warning).
Try running a 'summary', ploting etc.
On 15/05/12 23:51, Wang, Li wrote:
> 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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