In your OP, you show the following:
open (MYFILE, '148-N-pvalue0.01_peaks.xls');
#READ THROUGH THE FILE
while (my $line = <MYFILE>)
opening an Excel spread sheet this way will not give you access to the data you want. If you're are trying to parse an Excel spread sheet, consider using a module, like Spreadsheet::ParseExcel for the job. Otherwise, you can use "Save As..." within Excel to save the data as tab-delimited in a text file, e.g., "148-N-pvalue0.01_peaks.txt", which you can then open and process as above.
toolic shows how to obtain the last column's average, which includes using Acme::Tools. Importantly, two other pragmas begin the solution:
Consider always beginning your scripts with these, as they'll preemptively catch any problematic areas in your scripts--likely saving you many headaches.