I am struggling with the proper way to analyze my data. I did some research in and out of this forum but could not find the answer to my problem.

I am looking at neurons and trying to analyse the proportion of protrusions (called spines) co-localizing with a protein S. So for each neuron, I have a number of S+ spines and a number of S- spines. I analyzed this in 14 control neurons and 15 neurons from my experimental condition.

What I want to know is:

**Are the proportions of S- and S+ spines the same in my control and experimental conditions?**

You can see my data on the attached file below. Also, please note that the number of spines analyzed can be really different from one neuron to another (see last column of the attached file).

I tried normalizing the data as percentages (percentages of S- spines and S+ spines for each neuron) but I am not sure I can do statistics after I normalized the data that way. Also it seems wrong that a neuron for which I analyzed 43 spines would have the same weight as the one I analyzed 600+ spines for.

I also thought about using a binomial test on the raw data but I am not sure I can use my observed control data as "expected distribution". Can I? If so, that would mean I would have to pool the data from all neurons in each condition, would that be a problem?

If anyone had some insight to share on how to analyze these data, I would greatly appreciate it. Thanks.