Your code reassigns the entire contents of the array on each loop... if you want to collect it all inone large array, try this instead:

while(<FILE>){
  chomp;
  push @data, split(/,/,$_);
}
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...If you want individual arrays, you'll have to get fancier:

my @data = ();
while(<FILE>){
  chomp;
  push @data, [ split(/,/,$_) ];
}
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This will make an array of arrays, accessible as such:

print data[0][0]; # prints the first element of the first line
print data[4][3]; # prints the fifth element of the fourth line
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