These are questions regarding basic statistics/reporting in biology. I have already read a couple of articles on this subject, but couldn't find a clear answer applying to my research.
I have the following scenario:
I have 3 independent cell cultures from which I have analyzed 10 cells each with a confocal microscope and obtained a value X (protein interaction) for each measurement.
I also have 2 independent cell cultures from which I have analyzed 20 cells each obtaining value X again. These samples are my negative control.
Now I would like to compare these groups with a simple student's t-test and there are two thinkable scenarios:
(1) Average each independent sample's measurements as input for my statistical analysis: M1 (n=10), M2 (n=10), M3 (n=10) vs C1 (n=20), C2 (n=20) (n=3 for samples vs n=2 for controls).
In this scenario I would group all biological/experimental replicates together and compare them against all controls.
(2) Compare M1 (n=10) vs C1+C2 (n=40), M2 (n=10) vs C1+C2 (n=40), M3 (n=10) vs C1+C2 (n=40).
In general, this appears to me like comparing independent Day 1, Day 2 and Day 3 of an experiment to a control.
Q1: Would it be better to compare to C1 only instead of C1+C2?
In this scenario I would compare each biological replicate with the controls. This seems more appropriate to me, as an overall/grouped result could be heavily affected by errors.
Q2: But which solution is appropriate? Q3: Are these measurements for each independent cell culture technical replicates even though they are not performed on the same cell?
EDIT: As an alternative, I could report just the first experiment as add "Experiment was repeated with similar results" as seen in various publications. However, this appears to be the worst solution to me.
Thanks in advance!