Index: /branches/pap_branch_080320/ppMerge/src/ppMergeLoop.c
===================================================================
--- /branches/pap_branch_080320/ppMerge/src/ppMergeLoop.c	(revision 17168)
+++ /branches/pap_branch_080320/ppMerge/src/ppMergeLoop.c	(revision 17169)
@@ -219,4 +219,18 @@
                 }
             }
+
+            // Get list of cells for concepts averaging
+            psList *inCells = psListAlloc(NULL); // List of cells
+            for (int i = 0; i < numFiles; i++) {
+                psListAdd(inCells, PS_LIST_TAIL, readouts->data[i]);
+            }
+            if (!pmConceptsAverageCells(outCell, inCells, NULL, NULL, true)) {
+                psError(PS_ERR_UNKNOWN, false, "Unable to average cell concepts.");
+                psFree(inCells);
+                psFree(outRO);
+                goto ERROR;
+            }
+            psFree(inCells);
+
             psFree(readouts);
 
@@ -283,4 +297,19 @@
         }
     }
+
+    // Get list of FPAs for concepts averaging
+    psList *inFPAs = psListAlloc(NULL); // List of FPAs
+    for (int i = 0; i < numFiles; i++) {
+        pmFPAfile *input = inputs->data[i]; // Input file
+        psListAdd(inFPAs, PS_LIST_TAIL, input->fpa);
+    }
+    if (!pmConceptsAverageFPAs(output->fpa, inFPAs)) {
+        psError(PS_ERR_UNKNOWN, false, "Unable to average FPA concepts.");
+        psFree(inFPAs);
+        goto ERROR;
+    }
+    psFree(inFPAs);
+
+
     if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) {
         goto ERROR;