You have an array or you have a file? If you are actually trying to modify an array, that is easy, if you are trying to edit a file, that is a little more difficult. And considering the nature of your post, I doubt your real hash/array/file is anything like what you posted, so trying to give you suggestions without knowing the true nature of the data/file/array/hash is almost useless.

I'm trying to edit a text file#1.
My file is like this
1 (tab) 001 (tab) 002 (tab) blah-blah

i turned that into an array with:
@Line = split(/\t/);

i made a Hash out of my other text file#2 which looks like:
001 yadda-yadda
002 yadda-yadda
if ($_ =~ /something/){
my $key = $1.;
my $genes = $3;
if ( defined ( $Genes{$key})){
$Genes{$key} = $3;
}
NOW, i want to take the value "blah-blah" and and substitute it in file#1

and i'm trying this, but doesn't work...
@Line = split(/\t/);
if ( $hash{$key} eq $Line[1] ){
s/$Line[1]/$Genes{$value}/g;

so that my file#1 ends up looking like
1 yadda-yadda 002 blah-blah

Since you have this same question on at least 3 perl forums I'll not continue to reply here too.

no problem... i didn't know all the forums were connected

answering me in any one of them is okay, thanks

All the forums are not connected, unless you count that you can connect to them all on the internet, but just like you found them to ask a question, the people that reply to perl questions can find them.