use strict;
use warnings;

my $in_file = shift @ARGV;  #in command line type the name of your file

open (IN, $in_file) or die $!; # open INPUT file
open(OUT, ">$in_file.multiplied.csv") or die $!; # open OUTPUT file to write in
while (my $line = <IN>){    #read file line by line

    chomp $line; #remove the end of line
    my @seq = split(/\s/, $line); # split line by space and populate an array
    my $name = shift @seq;  # remove first element of array (sample name)
    my @new_seq = map {($_)*3} @seq;     # multiple each element in array by 3 and populate new array
    # print write to OUTPUT file results in csv        
    #  format (can be opened with xcl):
    print OUT join ("\,", $name,@new_seq)."\n";
}

close IN;   #close INPUT
close OUT or die $!;    #close OUTPUT

Don't know why it happened but in while command should be: $line= <> IN between the <>

Ilia

If you don't mind moving beyond perl the following code will do the job using awk.

gawk '{printf "%s, ",$1; for (i=2; i<=NF; i++) printf "%d,",$i*3; printf "\n";}' infile > outfile