[R] Incomplete, unbalanced design, and pseudoreplication?

[Dieter Menne]

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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