R help - Jan 2007 - Error in heatmap()

Hi, 

 

I run into following error when using heatmap() for data matrix "xx".
Any help is appreciated? "xx" contains many "NA"s.

 
> hv <- heatmap(data.matrix(xx))
Error in hclustfun(distfun(if (symm) x else t(x))) : 

        NA/NaN/Inf in foreign function call (arg 11)

 

Thanks a lot.

 

Yuhong

 


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Dear Yuhong,

heatmap deals gracefully with sparse occurences of NA in the matrix, but 
will fail if whole rows or columns are NA. Try preprocessing your xx as 
follows:

xx = xx[rowSums(!is.na(x))!=0, colSums(!is.na(x))!=0]

  Best wishes
   Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
> Hi, 
> 
>  
> 
> I run into following error when using heatmap() for data matrix
"xx".
> Any help is appreciated? "xx" contains many "NA"s.
> 
>  
> 
>> hv <- heatmap(data.matrix(xx))
> 
> Error in hclustfun(distfun(if (symm) x else t(x))) : 
> 
>         NA/NaN/Inf in foreign function call (arg 11)
> 
>  
> 
> Thanks a lot.
> 
>  
> 
> Yuhong
>