Hi, I have run gcrma function to normalized my dataset through “command line gcrma”, affylmGUI and oneChannelGUI package. I got different result. “commad line gcrma” and affylmGUI gave similar numerical result. But oneChannelGUI give different result. Below are example results. The columns are my 8 array. The “command line gcrma 117_at 7.055748003 6.745033354 6.905952402 6.89984871 5.427986926 5.487144022 5.114700923 5.32301841 121_at 6.072564588 6.038053861 6.038053861 6.038053861 6.038053861 6.038053861 6.038053861 6.038053861 1255_g_at 2.184719955 2.184719955 2.184719955 2.184719955 2.184719955 2.184719955 2.184719955 2.184719955 affylmGUI gcrma 117_at 7.050791518 6.740370684 6.901693137 6.89418791 5.423481103 5.482261696 5.110524671 5.31888015 121_at 6.079636466 6.04510978 6.04510978 6.04510978 6.04510978 6.04510978 6.04510978 6.04510978 1255_g_at 2.184730201 2.184730201 2.184730201 2.184730201 2.184730201 2.184730201 2.184730201 2.184730201 oneChannelGUI gcrma result are 117_at 5.132868736 4.705035992 4.894346799 4.986446054 4.072583937 4.087168465 3.926364524 3.967091209 121_at 3.893796881 3.849060442 3.806120005 3.887322359 3.975799975 3.699148114 3.850412448 3.983149921 1255_g_at 2.38946722 2.518604015 2.418365149 2.281908869 2.309105889 2.296133099 2.21029538 2.272567028 Do they suppose to give identical output results as the input datasets are the same? I want to use other features from oneChannelGUI. But I want to make sure that it gives correct normalized result first. Thanks for the help ying This information is directed in confidence solely to the person named above and may not otherwise be distributed, copied or disclosed. Therefore, this information should be considered strictly confidential. If you have received this email in error, please notify the sender immediately via a return email for further direction. Thank you for your assistance. [[alternative HTML version deleted]]