Dear BioConductor list: I started to learn limma function for giving weight to all Genepix flags less than -50. Also I tried to filter out spots that, for example, show the foreground/background ratio less than 1.2. I am wondering whether or not: 1. I can set two different weight values in my data set, e.g. 0.5 for $Flags == -50 and 0.1 for $Flags == -100 with a function? 2. I can perform flag weighting and forground/background weighting described above at the same time when reading data in? Or are there any other ways to do that? I will appreciate it if you could help me out! JP- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Jianping Jin Ph.D. x x Bioinformatics scientist x x Center for bioinformatics x x 3133 Bioinformatics Building x x CB# 7104 x x University of North Carolina x x Chapel Hill, NC 27599 x x Tel: (919)843-6105 x x Fax: (919)843-3103 x x E-mail: jjin at email.unc.edu x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx