I need to do Differential expression analysis of microarry data I am stuck at one point. What I need to do is extract Up-regulated and down-regulated miRNA's from my data frame. I have data frame with 5 Samples A,B,C,D,E. A is parent (reference)sample and rest of samples are from patients. each row represents a miRNA and value against that row in each column represents Back ground subtraction values of that miRNA in each sample. so on the basis of this I want to extract miRNA's which are up regulated and down-regulated in each sample. I can do pairwise comparison like I can compare A&B, A&C A&D A&E or I can compare all sample at the same time like Name A B C D E.
My Data frame look like
A B C D E
miRNA-168 20.44 60.55 2. 11 5. 77 300 2.07.
miRNA-170,miRNA-70 13.5558 58.558 3.857 8.748 89.97465
and so on