I have done proteomics and I have obtained genes with ratios. As an small example you can see my data below
Gene Control1 Control2 Control3 Treated1 Treated2 Treated3 pps-1 324680000 211350000 356350000 269770000 258080000 292830000 R11A8.7 477490000 610780000 539550000 533590000 530810000 578290000 ugt-21 105080000 103430000 74137000 78915000 42381000 31415000 spp-18 1042800000 615030000 332720000 538340000 448280000 412310000
Now My question is that I have Three controls and Three Treated, Control has two biological replicate and Treated has two biological replicate
I am trying to find the pathways which the list of my genes activate it. I use IPA which is a tool for pathway analysis
How can I calculate the fold change for it? If I use the 6 values, IPA will give me 6 different results and then interpretation will lead me to hell.
I appreciate any help.