Dear,
In the preparations for publishing a manuscript, we have a big argument about the proper analysis of variance to compare multiple groups for a certain staining quantification.
We have two proteins (A and B) we know that they significantly promote a third protein (C) staining when they are added as a mixture than when they are added as individual proteins due to the effect of these two protein interactions (A & B) with each other which results in a conformational change in protein B. And we know that protein C does not interact with B, but it does interact with A.
Any way, now what we want to analyze is the change in protein A and B functions in the mixture if we remove a certain post-translational modification that occurs in protein A and in protein B as well. To remove that certain post-translational modification, we need to treat the proteins with X enzyme. One issue is that we cannot heat inactivate X enzyme after incubation with either proteins. Thus, when we added the protein mixtures either both treated or one of them treated to compare to the untreated mixture, we had the enzyme there and we included the protein buffer control with the enzyme added to make sure that the effect on protein C staining comes from removing the post-translational modification, not from the remained enzyme with the added proteins to cell cultures.
Now, we have a dataset which has been arranged based on the independent variables in a way to analyze the differentiation in protein C staining (dependent) between the dataset groups. I am very convinced that we do not have in the given dataset a proper/consistent classification for any subcatagories in this dataset to analyze suitable for two-way anova. To me, the dataset are suitable for one-way anova if we consider the protein mixture as one protein (one variable) wither treated or not; otherwise, three-way anova if we consider each protein as a different variable when each is either treated or not. The images below are for the same dataset but with different variable arrangements on the datasheets.
Please, inspire me.
Thank you