Hi Colleen,

I usually perform statistical analyses using SPSS. In this particular case, I would apply a two-way ANOVA (genotype and treatment). This kind of analysis would let you unravel potential interactions between both factors. If you get an interaction, you could then handle each genotype separately, by running a split file, to further elucidate the specific effects of the treatment by means of a one-way ANOVA (treatment). 

I hope I've helped!

Fiona

Hi,

As mentioned earlier, two-way ANOVA. Although I use Graph pad, but even in SPSS it is good. Then you may use post tests if you like.

A two-factor ANOVA would do (as alredy mentioned) with treatment and genotype as main factors, both treatment and genotype as within subject fators since you say the factors are independent. This allows you analyse all data at the same time hereby reducing alpha errors,  if the software is good (e.g EZANOVA)  it wil als give you pairwise comparisons after Tukey HSD posthoc analysis. you would then be free to pick the comprisons that relate to your study