Index: trunk/ippScripts/scripts/lap_science.pl
===================================================================
--- trunk/ippScripts/scripts/lap_science.pl	(revision 32507)
+++ trunk/ippScripts/scripts/lap_science.pl	(revision 32534)
@@ -457,12 +457,17 @@
 	    my $exp_B = ${ $exposures }[$indexing{$exp_id_B}];
 	    print "$exp_A $exp_B $exp_id_A $exp_id_B $indexing{$exp_id_A} $indexing{$exp_id_B}\n";
-	    $exp_A->{pairwise} = 1;
-	    $exp_A->{pair_id} = $exp_B->{chip_id};
-	    
-	    $exp_B->{pairwise} = 1;
-	    $exp_B->{pair_id} = $exp_A->{chip_id};
-	    
-	    if ($verbose) {
-		print "LAP_DIFFS: $object: $exp_A->{exp_id} and $exp_B->{exp_id} are a pair\n";
+	    if ($exp_A->{diff_id} == $exp_B->{diff_id}) {
+		$exp_A->{pairwise} = 1;
+		$exp_A->{pair_id} = $exp_B->{chip_id};
+		
+		$exp_B->{pairwise} = 1;
+		$exp_B->{pair_id} = $exp_A->{chip_id};
+		if ($verbose) {
+		    print "LAP_DIFFS: $object: $exp_A->{exp_id} and $exp_B->{exp_id} are a pair\n";
+		}
+	    }
+	    else {
+		$exp_A->{pairwise} = 0;
+		$exp_B->{pairwise} = 0;
 	    }
 	}