Incomplete, unbalanced design, and pseudoreplication?
Jennifer Mollon wrote:
The response is a measurement - the amount of DNA extracted during the experiment. There were 2 factors to be tested - one is the condition under which the experiment took place and the other is the type of DNA to be extracted. Each set of factors was replicated, so condition A and DNA type A were tested twice using the same input material. Finally, the whole experiment was repeated twice, but in one of the experiments there was not enough input material and one of the DNA types (call it type D) was not tested at all, but all other levels of that factor and the condition factor were tested. From this, I think: ....
This is a classical case for procedure lme in package nlme which is quite robust for unbalanced designs. Arrange your data in the long form; preferably use characters instead of numbers to describe the levels. Check the book by Pinheiro/Bates for details; or, as a starter, the examples in library/nlme/scripts. Dieter Condition DNA Run Amount CondA DNAA Run1 33 CondA DNAB Run1 22
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