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
How can I calculate the fold change for it?
I see two ways
The first way I take the average of my control group , lets call it A (one column) I take the average of my treated group, lest call it B (one column) Then I calculate the fold change (B/A)
This way, I can check also whether the correlation between all biological replicate of control or treated are high which indicates taking the average is fine
The second way I perform multi comparison test on both group I find up regulated genes and down regulated genes I discard the rest of the genes I take the average of my control group , lets call it A (one column) I take the average of my treated group, lest call it B (one column) Then I calculate the fold change (B/A)
which one of them make more sense?
My main concern is how to calculate the fold change when I have biological replicate ,
I posted in biology group they said it is better I post it here
How then can one calculate p-values for fold change if it is based on average