[BioC] Contingency tests in R, Error with large numbers

[Gibbons, John G]

   Hello,
   I am fairly new to R though, so please forgive me if this is a fairly easy
   solution.
   I  am  trying  to  perform  multiple Fisher's Exact tests or Pearson's
   Chi-squared contingency tests from a datamatrix in which data from each row
   is data for an independent test.
   My data is formatted as such:
   Quote:
   AAA 75533 4756922556 88210 6715122129
   BBB 14869 4756983220 16384 6715193955
   CCC 7230 4756990859 8559 6715201780
   DDD 18332 4756979757 23336 6715187003
   EEE 14733 4756983356 16826 6715193513
   FFF 2918 4756995171 3433 6715206906
   GGG 3726 4756994363 4038 6715206301
   HHH 6196 4756991893 7011 6715203328
   III 7925 4756990164 9130 6715201209
   JJJ 1434 4756996655 1602 6715208737
   Where the 1st column is the identifier, the 2nd column = observations 1, the
   3rd column = background counts 1, the 4th column = observations 2 and the
   5th column = background counts 2. As you'll notice, the observed frequencies
   are MUCH larger than the background frequencies.
   I am loading my data like this:
   > data=read.table("My.File", header=FALSE)
   And I am looping through each row to perform a test like this:
   > pvalues=c("pvalue")
   > for(i in 1:10){
   + datamatrix=matrix(c(as.integer(data[i,2:5])),nrow=2)
   + fisherresult=fisher.test(datamatrix)
   + pvalues=cbind(pvalues,fisherresult[1])
   + }
   Here is the Error I am Getting:
   Error in fisher.test(datamatrix) :
   all entries of 'x' must be nonnegative and finite
   In addition: Warning messages:
   1: In matrix(c(as.integer(data[i, 2:5])), nrow = 2) :
   NAs introduced by coercion
   2: In matrix(c(as.integer(data[i, 2:5])), nrow = 2) :
   NAs introduced by coercion
   When I replace the large number in the 3rd and 5th column with smaller
   numbers, the statistical calculation works fine.
   Any ideas? Any help would be GREATLY appreciated!
   Thanks,
   John
   ------------------------------------------
   John G Gibbons, Ph.D.
   Postdoctoral Research Fellow
   Lemos Lab
   Harvard School of Public Health
   Department of Environmental Health
   665 Huntington Ave
   Building 2
   Boston, Massachusetts 02115
   Phone: 617.432.4991
   Email: jgibbons at hsph.harvard.edu
   http://www.hsph.harvard.edu/john-gibbons/