Hello all,

I have cultured three population of cells with a different antibody treatments (X, Y, Z) and a population with one isotope control (I). We also have a baseline control (B) of cells before culturing.

Is it possible to subtract effect of the isotope control from antibody treatment before comparing to baseline:

(X - I) vs B

Additionally can I make these comparisons:

(X - I) vs (Y - I) vs (Z - I) vs B

Many thanks!

Think about these in terms of log counts. You want to compare the log ratio of X to I directly to the log counts of B? I'm not sure that makes sense.

Maybe think through an example gene with hypothetical counts to see what comparison you want.

Suppose X has counts of 100, I has counts of ...