Which statistical test to use for two groups of patients?

Question

[felipead66]

I have RNA Seq for 2 groups of patients, Group1 with 4 patients and Group 2 with 5 patients. I want to find differences between the two groups (Grouo1 vs Group2) as well as whether a gene is up- or down regulated in one group vs the other. A first thought would be to use the Mann-Whitney test.

In order to limit the results I would like to do other tests and focus on the common results (the intersection). What other alternatives would I have?

Answer 1

[ATpoint]

Please use the established packages for RNA-seq differential analysis. Most common choices are limma, edgeR and DESeq2, all of which have extensive manuals, are well-maintained, tested and accepted. Do not do any homebrew statistics as elaborate frameworks exist that take care of the necessary steps such as normalization, dispersion estimation, model fitting, multiple testing correction etc.

[felipead66]

You are right regarding the RNA Seq, what I should clarify though is that I have single-cell RNA Seq therefore I could not limit to those common choices. Moreover, I have normalized data rather than gene counts.