FFT analysis of binned data of different length I am conducting experiments to collect wind speed data from wind anemometers placed on a moving platform. Closely, there is a fixed wind mast holding a wind vane. Prior to analysing the wind data from the moving platform, I binned the data with 1-minute average wind direction. Each bin contains a number of continuous data sets (Set 1, Set 2, Set 3 etc.) which may not necessarily have the same number of data points. For example, Set 1 has 20,000 data points, Set 2 has 6,000 data points, etc.

I am performing an FFT on each of the sets to detect any periodicities in the signal. I am plotting the real amplitude of the sinusoids present in the signal on the y-axis vs. the frequency of the sinusoid. The FFT of each data set is yielding different amplitude results, on the y-axis and I'm not sure whether this is a result of the different length of the arrays. I am interested in an average value of the y-axis of the spectrum. However, I don't think that it is suitable to just calculate the average due to the different array size. Can someone please suggest a method? I am not used to analysis of signals in this way so I'm a bit confused. Thanks a lot.
Let's say you have several data sets $x_i$ and $N_i$ is the length of the $i$th data set.

First you're right that the amplitude of the FFT output scales with its length. To normalize all data sets they have to be divided by $N_i$. (Note that depending on the implementation of the FFT there might be a scaling involved already, check the Doc or see this question)

To combine all data sets you should append $(\max_i N_i) - N_i$ zeros to every data set before taking the FFT. The frequency axes are then aligned correctly and you can calculate the average of all FFT outputs.

Btw, I would plot the absolute value of the FFT output, not the real part. And sometimes I find it useful to "smooth" the spectrum by averaging every $M$ neighbouring FFT bins. Last, I have assumed that the data of every set has been acquired at equidistant time steps, otherwise the FFT isn't applicable at all.