Certain amount of material is injected in animals, say proteinA, proteinB .... proteinZ, and measurements were made on the corresponding amount recovered. Would have been nice to inject equal amounts and do stats on how much was recovered, increase/decrease etc. and corresponding effect sizes. But that is not possible given experimental constraints, so proteins A, B, C, D all had different original amounts, different by several orders of magnitudes, say 1 unit, 100 unit or 10000 unit.
Eventually need to compare the proteins with each other, which has best performance in the experiment, i.e. best recovery compared to injected amount. Currently using log2FC, and getting a single value for each protein, say 5-fold protein A, 10 fold protein B, -2 fold protein C, so on and so forth. this gives some qualitative assessment of which are doing best compared to others. Using MA plots to factor in amount of material as well.
But I now need to compare between the proteins, to say something like how much better (or worse) proteinA is compared to proteinZ. Taking ratios of Log2FC, is that fair? Any stats anyone can recommend?
Granted it is not ideal scenario, but need to provide some inference based on the the measurements so any suggestions are welcome.