There are two factors of time, but they are evenly replicated across all the
other factors/levels.  The experiment is perfectly balanced except for one
lost sample, which is deleted automatically in the aov.  I am very certain
the analysis is correct.  I think its merely a discrepancy between how aov
and TukeyHSD group the levels of the factor variable. Probably aov handles
any vector specified as a character vector, whereas TukeyHSD merely assumes
its a character vector.

It might be something to refine in the stats package so the functions, which
are designed somewhat to be used together, can work on the same kinds of
data.

On Tue, Oct 20, 2009 at 6:13 PM, Richard M. Heiberger <rmh@temple.edu>wrote:

> Now I am worried that you have a wrong analysis.
> the aov function is perfectly happy using either factors or
> numeric variables.  Are there really only two levels of time,
> which is what one degree of freedom for time suggests?  Or are there
> more than two level, but since aov() sees that as a numeric variable
> it has only one df.
>
> csv files can interfere with the interpretation of data values, but
> not likely in this case.  They too will have numbers interpreted
> as numeric.
>

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