I am unsure about how to analyze some data of my PhD project and could use some input. I am analyzing data from a Phase I clinical trial where we have scRNAseq + Histology of paired PRE and POST biopsies. However, as the clinical trial was stopped early due to outside reasons (adverse effects in a different trial in a different condition), I am left with "only" 5 paired samples. Now, I want to compare fractions (e.g. Number of CD8+ T cells/mm2, or %of stromal coverage, or % of total population) between PRE and POST to see where the treatment induced changes. In some cases, it seems quite clear as there is a strong difference, however I don't know which statistical test to apply.
Normally I would say the Wilcoxon matched-pairs signed rank test, since I don't think I can assume normality for fractions. However, with 5 paired samples, the power is too low to reach significance threshold (lowest attainable p value with wilcoxon with N=5 is 0.0625), which in principle I don't care about since I think there is still a pretty strong message when I see the same effect in scRNAseq and histology, but I am worried that it will make submission more difficult. I have also seen people use the paired t-test for these kinds of fractions in the literature in good journals (e.g. Cell), but I think that would be cheating (but I'm hoping to be wrong here - please tell me).
If you have other ideas, feel free to let me know. If there's some special test for low N paired samples not assuming normality that is not available in Graphpad, I am fine with R as well.
Thank you all!!
