[BioC] Deciding on a cut off after QC

[Ankit Pal]

Dear All,
I'm using LIMMA to analyse a set of GPR files.
I used the weight fuction to apply QC parameter
threshold values recommended by Genepix.
The code for the same is

>myfun <- function(x,threshold=55){
+ okred <- abs(x[,"% > B635+2SD"]) < threshold
+ okgreen <- abs(x[,"% > B532+2SD"]) < threshold
+ as.numeric(okgreen & okred)
}

 On completion of the analysis, all the spots showed
up in the results file inspite of being flagged off. I
understand that on being flagged off by limma (wt =
0), the spots are not considered for further analysis.
Is there any way they can be excluded from the final
result file. 
Also, if I get an output of all the spots (38000 in my
case) how do I decide on a cut off. Do I use the rank
or something else?
Waiting eagerly for a reply,
thank you,
-Ankit