Finally I found the solution,
I am posting this answer to help other people having the same doubt.
Instead of directly specifying the array in the cypher query , you could use it like this
$id=[12344,546674,6789];
$client = new Everyman\Neo4j\Client();
$query= "match (u:user{id:".$user_id."})-[r:knows]->(c:data)
set r.id={myid}";
$result = new Everyman\Neo4j\Cypher\Query($client, $query,array('myid' => $id));
Hope this helps, Thank you