I have the normalized data with approximately 300 genes and 50 paired samples (Before vs After metabolite levels). In addition, I have the another column with the Group A, B, and C grouped or assigned based on the metabolite level. I am interested to perform t-test between the two groups (Before vs After) and 1-way ANOVA to compare the groups A vs B vs C. When I perform the statistical test between Before vs After or ANOVA between A vs B vs C, the output displays one p-value, however, I am interested in obtaining p-values for all the genes with the FDR for my datasets. I used the below functions in R to perform the same. Is there specific package to perform this?
Example of the data grouping.
Samples Metabolite_Level Group Sample_1 Before A Sample_2 Before B Sample_3 Before A Sample_4 Before B Sample_5 Before B Sample_5 Before B Sample_6 Before A Sample_7 Before C Sample_8 Before C Sample_9 Before C Sample_10 Before A 2_Sample_1 After A 2_Sample_2 After B 2_Sample_3 After A 2_Sample_3 After A 2_Sample_4 After B 2_Sample_5 After B 2_Sample_6 After A 2_Sample_7 After C 2_Sample_8 After C 2_Sample_9 After C 2_Sample_10 After A