[R] Issue with write.table and read.table : I'm not getting out what I put in

[Irina]

Hello,

I am trying to save a large matrix of values in a file. My problem is that I am
writing 
write.table(allpos,'control_chr1.txt', dec=".")
and then I want to check it with
test2=read.table('control_chr1.txt')
sum(test2[,2]==allpos[,2])

This last number is lower than the length of the test2[,2] vector. This is
really annoying me because I can't figure out why I don't get out the same thing
that I put in.