Hi all,
I have a 6 case and 6 age-, gender-matched control human brain snRNA-seq data (one-to-one matched). All samples were integrated and analyzed together, and I would like to compare the difference in cell proportion between control and case.
At this time, I am confused whether I should perform a paired t-test or an unpaired t-test. If it was a DEG analysis in RNA-seq, a paired t-test would have been performed, but it is a concern because it is a cell proportion comparison in snRNA-seq.
Although it is a mathced sample, it is thought that sample variation, technical variation, capture efficiency, etc. in snRNA-seq may affect cell number and cell proportion. So I don't know which of the two methods below is more suitable.
1) Paired t-test
2) Unpaired t-test + beta-regression (or multiple linear regression) to estimate the contribution fo the sample clinical features (ex. disease status, Age, gender, PMI ...) on the cell proportion variation.
Thanks in advance!
Joonhong Kwon
