[BioC] spot weight in limma

[Ren Na]

Hi,
Our 16k mouse array has five types of spot, one of them is "empty" type, 
which means it is just buffer, no oligo in this type of  spots. After I 
used the function read.maimages like:
RG <- read.maimages(targets$FileName, source="spot", wt.fun=wtarea(100))
I checked the weights assigned to the "empty" type of spots, most are 
0.2 to 0.35, but some of them are around 0.5 to 0.7, and  I also can 
find 0.8 or 0.9. Then I  went back to check the image(tiff file). For 
the "empty" type of  spots which have been asigned high weight, I can 
see nothing or just very tiny dot comparing with "oligo" type of spots.
My question is: wtarea downweights spots which are smaller. Those 
"empty" type spots should get weights close to 0. Where I did 
incorrectly ?  I greatly appreciate any advice.
My another question is: we have a batch of slides, it is supposed to 
have 16 k spots. But 600 spots were not printed on those slides at all 
because of machine problem. Here my question is: can I assign weight 0 
to these 600 spots after I get RGList? or I treat them as "empty" spots 
and use the function like above?

Thanks in advance,

Ren