3

I have a set of integer that I am trying to see use different methods to categorize them into four groups, and the 2x2 table for the outcome of the 2 methods is displayed as below:

                method_B
     method_A   0   1   2   3
            0 182  11   0   0
            1  41 127   2   0
            2   0  12  18   0
            3   0   0   0   4

I am thinking of using chisq.test for comparing whether the difference in grouping distribution produced by 2 methods are likely to be caused by chance, but I am worrying about too many zeroes in the 2x2 table.

Should I use chi.sq test? Or is there any equivalent fisher.test for my case?

P.S. I tried fisher.test but it gives me FEXACT ERROR 501, which I have no idea what it is.

lokheart
  • 3,199
  • 9
  • 40
  • 49
  • Try increasing the workspace argument of fisher.test. That may avoid the error message, if your computer has enough memory (and you have enough patience). See ?fisher.test. See my previous answer http://stats.stackexchange.com/questions/4023/chi-square-test-for-equality-of-distributions-how-many-zeroes-does-it-tolerate/4029#4029 – onestop Feb 14 '11 at 08:27

1 Answers1

2

I don't think either chi-squared test or Fisher's exact test is useful here. It's pretty obvious that the results from method A and from method B aren't independent of each other. A statistic to quantify how well the two methods agree is more useful. The obvious choice is Cohen's kappa.

onestop
  • 17,737
  • 2
  • 62
  • 89