Hi BioC, I am using Limma, the problem occurs in my 2nd object RGgpr$genes$Status. > SpotTypes SpotType controltype Name color 1 cDNA * * black 2 genes FALSE * grey 3 positive positive * blue 4 ignore ignore * orange 5 notprobe notprobe 0 yellow > RGgpr$genes$Status <- controlStatus(SpotTypes, RGgpr$genes) Matching patterns for: Name Found 11592 cDNA Found 11592 genes Found 11592 positive Found 11592 ignore Found 664 notprobe Setting attributes: values controltype color I cut and pasted two columns (Name and controltype) of *.gpr files to confirm the different numbers of controltypes. >table(read.table("twoColumns.txt",sep='\t',header=F)) FALSE ignore notprobe positive 8564 2112 664 252 Q1, Why did they give me the same # 11592 ? Is it because I used wild card "*" ? Can this be fixed? Q2, If so, what can i do with the SpotType.txt to fixed the problem ? Thanks for any help Kevin