Fig 1C of the Replication Study: Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET uses an odd (to me) three stage normalization procedure for the quantified western blots. The authors compared blot values between a treatment (shMet cells) and a control (shScr cells) using GAPDH to normalize the values. The three stages of the normalization are
first, the value for the Antibody levels were normalized by the value of a reference (GAPDH) for each Set.
Some background (due to Sewall Wright’s method of path analysis) Given a generating model:
\[\begin{equation} y = \beta_0 + \beta_1 x_1 + \beta_2 x_2 + \beta_3 x_3 \end{equation}\] where \(x_3 = x_1 x_2\); that is, it is an interaction variable.
The total effect of \(x_1\) on \(y\) is \(\beta_1 + \frac{\mathrm{COV}(x_1, x_2)}{\mathrm{VAR}(x_1)} \beta_2 + \frac{\mathrm{COV}(x_1, x_3)}{\mathrm{VAR}(x_1)} \beta_3\).
If \(x_3\) (the interaction) is missing, its component on the total efffect is added to the coefficient of \(x_1\).
This post is motivated by a twitter link to a recent blog post critical of the old but influential study An obesity-associated gut microbiome with increased capacity for energy harvest with impressive citation metrics. In the post, Matthew Dalby smartly used the available data to reconstruct the final weights of the two groups. He showed these final weights were nearly the same, which is not good evidence for a treatment effect, given that the treatment was randomized among groups.
