Hello, On my microarray, I have different number of probes for each gene (some have 2 probes and some have 3 probes), For example: Probe1 Gene1 Probe2 Gene1 Probe3 Gene2 Probe4 Gene2 Probe5 Gene2 Probe6 Gene3 Probe7 Gene3 ....... If I use "lmFit" in LIMMA package to fit the linear mode, there is a problem because I can not define single "ndups", I'm not sure if I can still use this function, or I have to re-organize the data for using this function? Are there other functions I can use to solve this problem? Any suggestions appreciated. Yi Zou