I have a similar problem ....

I get the warning message "Argument "n" isn't numeric in array element at program.pl line 356."

My code looks like this:

foreach $qbase (@query_sequence [$q_start .. $q_end])
    {
        if ($qbase eq ("n"||"N") && $subj_sequence[$qbase] ne ("n"||"N
+"))
        {
            ++$ncount;    
        }
    }

    foreach $sbase (@subj_sequence [$s_start .. $s_end])
    {
        if ($sbase eq ("n"||"N") && $query_sequence[$sbase] ne ("n"||"
+N"))
        {
            ++$ncount;
        }
    }
[download]

My code is intended to mean:
for each position between a start and end position in an array, if the element at that position is an 'n', and the element at the same position in another array is not an n, ++count. $q_start, $q_end, $s_start, $s_end are numbers. @query_sequence and @subj_sequence are arrays of letters. It works ok apart from the warning! Why does this happen and how do I fix it?

Many thanks for your help

Marinegirl x