I'm sorry, I do not understand this part...abit lost here:

for my $key ( keys %hash ) {
        if ( $key =~ /^dataS\d\dR\d$/ ) {
            print $key, @{ $hash{$key} }, "\n";
        }
[download]

I want to be able manipulate the columns individually (thus attempting array) so I am not sure how hash can help in this case. I try running it but there's error which the script keep running without stopping. Instead, I attempted the matching of the colume names by using loop but I run into errors somewhere. I have my own code where I did a while loop to find the matching headers:

my $first = 1;
for(my $i = 0; $i < $originalfilecount; $i++)
{
    #read in the current file
    open CURINFILE, "<$files[$i]" or die "Error couldn't open file $fi
+les[$i]\n";
    print "$files[$i]\n";
    if($first)
    {
        #if this is first file, find column locations
        my $firstline = <CURINFILE>;   #read headerline
        chomp $firstline;
        my @columns = split (/\t/, $firstline);
        my $columncount = 0;
        
        # print "$firstline\n"; #check if print headers correctly

####### Column Headers for ID, TIME #########     
       
        while ($columncount <= $#columns && !($columns[$columncount] =
+~ /ID/))
        {
                $columncount ++;
        }
        $ID = $columncount;
        while ($columncount <= $#columns && !($columns[$columncount] =
+~ /Time/)) 
        {
                $columncount ++;
        }
        $masstimes = $columncount;
              while ($columncount <= $#columns && !($columns[$columnco
+unt] =~ /Links/)) 
        {
                $columncount ++;           
        }
        $Links = $columncount;

#check if column position is correct (so far it is correct)      
print "ID is at column: $ID\n"; #output = 0
print "Time is at column: $masstimes\n"; #output = 1
print "Links is at column: $Links\n"; #output = 33
       
#DataR Columns (got ERROR here where I can't run script at all if I ad
+d this) #

        while($columncount <= $#columns && !(($columns[$columncount] =
+~ /_data/)))
        {
            $columncount++;
        }
        
        $columns[$columncount] =~ /_dataS(\d+)R/;
          my $currentReplicateID = $1;
    my $currentReplicateCount = 1;
        $ctrlStartCol = $columncount++;
        while($columncount <= $#columns)
        {
            $columns[$columncount] =~ /_dataS(\d+)R/;
            my $newReplicateID = $1;
            if($newReplicateID ne $currentReplicateID)
            {
                push(@replicateCount, $currentReplicateCount);
                 $currentReplicateID = $newReplicateID;
                 $currentReplicateCount = 1;
            }
            else
            {
                $currentReplicateCount++;
            }
            $columncount++;
        }
        #add the last replicate in
        push(@replicateCount, $currentReplicateCount);
              
        
 ###### End of Data Column Headers ####     
   


####### Read remainder of the file ##############
        while (<CURINFILE>)
        {
            #add metabolite ID, MZ, RT to an array
            chomp $_;
            my @templine = split (/\t/, $_);
            push(@tempratio, $templine[$metabolite]);
            push(@tempratio, $templine[$masstimes]);
            push(@tempratio, $templine[$rt]);
            
            #ERROR
            #add intensities from the samples
             my $columnIndex = $ctrlStartCol;
                for(my $k = 0; $k <= $i; $k++)
        {
                    $columnIndex += $replicateCount[$k];
        }
                    for(my $j = 0; $j < $replicateCount[$i+1]; $j++)
                    {
                        push(@tempratio, $templine[$columnIndex+$j]);
                    }       
         
        }

} # end of main if loop 



close CURINFILE;
} #end of main for loop 

    
       
  ############## Start of output ##################      
                                         
                     
print "\nWriting output...";

#create a new Directory and open output files and print out those valu
+es from the hash that meet the filtering criteria
#filtering criteria: defaults set at pvalue < 0.05, 0.5 <ratio > 1.5. 
+User specified
mkdir "$pathname" or die "Error couldn't create new Directory";
open my $OUT1, ">$pathname/Metabolite ID.txt" or die "error couldn't o
+pen output file";
open my $OUT2, ">$pathname/masstimes.txt" or die "error couldn't open 
+output file";
open my $OUT3, ">$pathname/retentiontimes.txt" or die "error couldn't 
+open output file";
open my $OUT4, ">$pathname/intensitydata.txt" or die "error couldn't o
+pen output file";

print $OUT1 "$tempratio[0]";  print $OUT2 "$tempratio[1]";
print $OUT3 "$tempratio[2]";
print $OUT4 "$tempratio[3]";


close $OUT1;
close $OUT2;
close $OUT3;
[download]

PS: The output only print 1st value for all OUT1 to OUT4 instead all the values in the whole columns...why?? my DataR names are something like this across the columns:

8899_Neg_Rep01_dataS01R01
8889_Neg_Rep02_dataS01R02
8889_Neg_Rep03_dataS01R03
7499_Neg_Rep01_dataS02R01
7499_Neg_Rep02_dataS02R02
7499_Neg_Rep03_dataS02R03
7709_Neg_Rep01_dataS05R01
7709_Neg_Rep02_dataS05R02
7709_Neg_Rep03_dataS05R03

(and so on...)
[download]

That's why I attempt a while loop to try match but I think somewhere is wrong? Not sure if it is the right way to do this.

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