With all due respect, I have to differ.
There's a problem using two magnets when there's e.g. two groups, because any purported effect of group _could_ be confounded with the effect of magnet. In that case, my impression is that the appropriate remedy is to test the groupXmagnet interaction and show that it's not significant at a very liberal p level (at least in the areas of interest).
Here, the OP states that he's looking at one group only. While the effect of magnet in this case isn't explicitly accounted for, in terms of means alone (not looking at df), it just means "here's the mean effect, where this fraction of the sample was collected on magnet 1, and this other fraction was collected on magnet 2." The lack of explicit accounting concerns what the proportion is.
In your solution (which is correct apart from my concern here), the two subgroups are weighted equally. While one could argue that this is in some sense better, it's not clear to me why it really matters as far as inferences of scientific (biological) interest are concerned. Obviously which magnet used has implications for results (e.g., raising field strength is usually thought to improve the ability of the instrument to detect results of interest), but usually not in ways which affect _validity_ of results (unlike the case of two groups). Of course, there are exceptions to this---in one dataset I worked on, the experiment was unfortunately not counterbalanced, and there was a peculiar artifact generated by that particular magnet and pulse sequence that led to an interaction with the presentation order...which generated faux results in the area of interest! But such concerns about validity even apply when using only one magnet.
Finally, to elicit the effect of magnet itself, the OP could use the [1 -1 ...] contrast representing the differences between the subgroups.
Cheers,
S
|