I want to use limma to identify differentially expressed genes. This is sample explanation.
A exosomes from parental - MCF7
B exosomes from resistant MCF7/Adr
C exosomes from resistant MCF7/Adr treated with Doxorubicins for 48 hours
D exosomes from resistant MCF7/Adr treated with Tipifarnib for 48 hour
E exosomes from resistant MCF7/Adr treated with Tipifarnib ..
this is my data frame
A B C D hsa-miR-199a-3p, hsa-miR-199b-3p NA 13.13892 5.533703 25.67405 hsa-miR-365a-3p, hsa-miR-365b-3p 15.70536 52.86558 18.467540 223.51424 hsa-miR-3689a-5p, hsa-miR-3689b-5p NA 21.41597 5.964772 NA hsa-miR-3689b-3p, hsa-miR-3689c 9.58696 44.56490 10.102051 13.26785 hsa-miR-4520a-5p, hsa-miR-4520b-5p 18.06865 28.06991 NA NA hsa-miR-516b-3p, hsa-miR-516a-3p NA 10.77471 8.039662 NA E hsa-miR-199a-3p, hsa-miR-199b-3p NA hsa-miR-365a-3p, hsa-miR-365b-3p 31.93503 hsa-miR-3689a-5p, hsa-miR-3689b-5p 24.26073 hsa-miR-3689b-3p, hsa-miR-3689c NA hsa-miR-4520a-5p, hsa-miR-4520b-5p NA hsa-miR-516b-3p, hsa-miR-516a-3p NA
Should I do pairwise comparison between A&B A&C A&D A&E?? same for B&C B&D B&E??
For Pairwise comparison I have to make a design and contrast matrix for that which I will use in lm function of limma. Can Any body can please guide me???
Suppose I have 1700 miRNAs in my data frame..