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john herbert ▴ 560@john-herbert-4612
Last seen 7.1 years ago
Dear all. I have been pondering about constructing a design matrix based on the Limma user guide, where I combine a time course with a paired analyses. The targets file looks like; Sample treatment time 1 control 24 1 control 72 1 control 0 1 treatment 24 1 treatment 72 2 control 24 2 control 72 2 control 0 2 treatment 24 2 treatment 72 3 control 24 3 control 72 3 control 0 3 treatment 24 3 treatment 72 Sample number refers to an individuals cancer cells, treatment refers to added drug or not and numbers are in hours (time elapsed). So it is a kind of paired, as patient variability is to be considered. The control sample at 0 is the same as treatment at time 0 as these are the same cells without any time/treatment. Please could someone help me understand how I can construct a design matrix and to understand how I can extract differently expressed genes that come about due to time, due to treatment and interaction of them both. Any pointers appreciated, though I am trying to see if the examples in the manual can be applied to this scenario. Thank you. John.