[R] how to remove NA/NaN/Inf in a matrix??

David Winsemius dwinsemius at comcast.net
Sun Sep 11 16:07:34 CEST 2011

On Sep 11, 2011, at 5:38 AM, anand m t wrote:

> Hi all..
> I'm very new R, and i'm analyzing microarray data using Bioconductor..
> Recently i was given microarray data to analyze. The problem is  
> whenever i
> run MAS5 presence calls algorithm,
> it throws an error saying NA/NaN/Inf in foreign function. How do i  
> remove
> such  NA/NaN/Inf's ??
> I tried na.omit(dataframe)  but stil problem exists.
> dimension of matrix (data) is 35556     7.
>> data.mas5calls=mas5calls(data)
> Getting probe level data...
> Computing p-values
> Error in FUN(1:6[[1L]], ...) :
>  NA/NaN/Inf in foreign function call (arg 2)

Besides the possibility that your data has NAs there is the possibilty  
that the authors of whatever package has that function did not  
anticipate some negative values or some other condition that your data  
led to. Maybe the "foreign function", i.e. not 'mas5calls'  tried to  
take the log of 0 or some such.

It's not possible to saymuch more given the vagueness of your  
question. This is also not the Bioconductor mailing list.

David Winsemius, MD
West Hartford, CT

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