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

 __________________________________________________



	[[alternative HTML version deleted]]

