Complicated design and therefore analysis
Eight treatments (2x4 factorial of germinated/not and 4 types of bacteria), 3 temperatures/chambers. Within each chamber there are 10 pots per treatment combination.
After the chamber, pots are set out in a greenhouse on a long shelf. They are organized so that the plants from each chamber are near each other. With a chamber, the pots are put in 10 blocks with one pot of each treatment in a block and the blocks are arranged on the shelf in order.
Each pot has 5 plants in it and the response variable is (typically) the number of plants that have disease.
How does temperature affect bacteria growth? How does germination affect bacteria growth?
Plot the data.
For the initial post-chamber measurements, conduct separate analyses for each temperature with fixed effects for germinated/not germinated, bacteria types, and their interaction. Assess qualitative differences between chambers and indicate these differences may be due to chambers or temperatures.
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