# read in lines across 20 files
while (1) {
my $batch1 = <FILE1>; chomp($batch1); 
last unless ($batch1);
...
my $batch20 = <FILE20>; chomp($batch4);

# put the lines into an array
# @batch_lines has 20 elements
push(@batch_lines, $batch1);
...
push(@batch_lines, $batch20);


#init the 2-array @confidence_mtx after parsing out some #data for the
# batch_lines elements

foreach (@batch_lines) {
  next if  /^Probeset/;
  my ($probe, $tmp) = split /\t/;
  push (@confidence_mtx, [ split /,/ , $tmp ]);
}

# do some lookups in the confidence_mtx data structure
my $batchnumber = $sample2batch{$consensus_sample_batch};
my $offset = $sample2offset{$consensus_samples_offset};

if ( $confidence_mtx[$batchnumber-1][$offset-1] > $CONFIDENCE_CUTOFF) {
  $consensus_genotypes[$i] = '00';
}

undef @confidence_mtx;

} # close while(1) loop