Dear all, I am comparing two time points (6 time points) data under different conditions. I want to look for genes that show different pattern under different conditions. I constructed contrasts as in the user's guide (diff=cond1-cond2 at all pairs of time points) and generated MArrayLM object okay. My questions come with decideTests with "nestedF". 1. how is the classification done exactly?? I found a much smaller set of genes using decideTests(nestedF, p=0.01) versus p.adjust(fit$F.p.value)<0.01 2. The TestResults matrix doesnt really make sense. for example, places where the matrix shows 1 as upregulation, dont necessarily have positive M value or doesnt show a p.value < 0.01?? What do I miss here?? really confused... 3. p.value and adjust.method parameter in the decideTests are applied to F stat or to the individual p value at each gene at each contrasts. I hope I made the questions clear. Need help desperately, since there's not much document on this. Other suggestions for this type of analysis are also welcome. Thank you. Lei Jiang Department of Chemsitry University of Washington Box 351700 Seattle, WA 98195 Phone: 206-616-6882 Fax: 206-685-8665

Dear all, I am comparing two time points (6 time points) data under different conditions. I want to look for genes that show different pattern under different conditions. I constructed contrasts as in the user's guide (diff=cond1-cond2 at all pairs of time points) and generated MArrayLM object okay. My questions come with decideTests with "nestedF". 1. how is the classification done exactly?? I found a much smaller set of genes using decideTests(nestedF, p=0.01) versus p.adjust(fit$F.p.value)<0.01 2. The TestResults matrix doesnt really make sense. for example, places where the matrix shows 1 as upregulation, dont necessarily have positive M value or doesnt show a p.value < 0.01?? What do I miss here?? really confused... 3. p.value and adjust.method parameter in the decideTests are applied to F stat or to the individual p value at each gene at each contrasts. I hope I made the questions clear. Need help desperately, since there's not much document on this. Other suggestions for this type of analysis are also welcome. Thank you. Lei Jiang Department of Chemsitry University of Washington Box 351700 Seattle, WA 98195 Phone: 206-616-6882 Fax: 206-685-8665