Comparing two ratios between two experiments.
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17 months ago
Vanish007 ▴ 40

Apologies in advance if this is a basic question, I think I’m making it out to be more complicated in my head than it needs to be. I wanted to make sure I was approaching it correctly:

I have two experiments with a treatment vs wild-type. Both were performed similarly, but one experiment was performed with a knockout gene and the other was not. So far I have performed a t-test within each experiment to test the outcome of the protein in treatment vs wild-type. My question is, would it be correct to compare the ratios of each experiment to the other through an odds ratio and then covert that to log odds and create a volcano plot? I want to look to see if their are differences in the protein expression outcome between the two experiments.

Hopefully this makes sense and I’m just over-complicating something that doesn’t need to be.

Thanks in advance!

comparisons phosphoproteomics ratios • 407 views
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Was WT one experiment and treatment one experiment, or do you have two WT vs treatment? Is this mass spec, if so I would strongly suggest to use a dedicated statistical framework such as DEqMS or DEP from Bioconductor rather than a simple t-test.

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I would have two WT vs treatment (one for each experiment) except that one experiment would also have a Knockout Gene and the other would not) - thereby would be a 2x2 comparison I believe.

DEqMS seems like a nice plan, however dealing with duplicate proteins in my rownames might be an issue that still does not have a proper solution aside from just making them unique IDs... hence why I am normalizing via log2 and then running a t.test..

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