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