In my game I want to make the player object transparent for 2 seconds by scripting at run time if the player collided with a specific object during the game ... is it possible ?
Check for collision. When the collision that you want is triggered then you can change the transparency.
GameObject g;
// 50% Transparency.
g.renderer.material.color.a = 0.5f; // a is the alpha value.
// 100% Transparency.
g.renderer.material.color.a = 1.0f;
You can do just this to make your program wait time: http://docs.unity3d.com/Documentation/Manual/Coroutines.html
You will notice the example is exactly your question.