Difference between of size in mapfile and mapscript

[Fu Chen]

Hi!
I really can't understand what's the difference between of size in mapfile and mapscript?
In php script, I try to setExtent and set "width" and "height" of mapobject to an output image.  
At first I guess the  "width" and "height" in script just replace the SIZE element in mapfile. But it's wrong. If I change the size in the mapfile but keep the value in script not changed, I get quite different result images. 
I dont know what's the relation of those variables. 
Can anyone give me a hint?
Thank you!

some statement in my script:

$gpoMap->setExtent($minx, $miny, $maxx, $maxy);

$dfWidthPix = $w;
$dfHeightPix = $h;
$gpoMap->set("width",$dfWidthPix);
$gpoMap->set("height",$dfHeightPix);