[BioC] warning message in KS test

[Francois Pepin]

Hi James,

Please note that there is nothing bioconductor specific in this
question. You might want to use the R-help list instead next time. You
are more likely to get a useful answer from there and it reduces the
clutter on this one.

This being said, a warning is not an error, you should still get a
result. The warning simply means that the KS test will not give an exact
pvalue if you have identical values in one (or both) of your
distribution. You still get an estimate that I've found to be usable
when I've used it.

Francois

On Thu, 2007-10-18 at 15:37 -0700, James Anderson wrote:
> Hi, 
> 
> I am trying to use ks test to do gene selection for microarray data. 
> Suppose A is my matrix with 5000 genes and 60 samples, the first 30 samples are in class 0, the other 30 samples are in class 1. 
> 
> I use the following command to calculate the pvalue for each gene. 
> 
> index_class0 = which(ClassLabel == 0)
> index_Class1 = which(ClassLabel == 1)
> PvalsAll <- apply(A, 1, function(x) ks.test(x[index_class0], x[index_class1],
> exact = NULL)$p.value)
> 
> I got some warning message like:
> 
>  In ks.test(x[index_class0], x[index_class1], exact = NULL) :
>   cannot compute correct p-values with ties
> 
> but with the same data, I can get some values using matlab statistics toolbox, does anyone have similar experience? How to fix this problem?
> 
> Many thanks,
> 
> James
> 
>  __________________________________________________
> 
> 
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