thefatih

What difference in estimated effect size would be large enough to change the interpretation you're trying to preserve? Your clarification settles which quantity matters, but leaves the meaning of stability open. A claim that the estimates are close needs an explicit tolerance before we can decide whether a difference across normalization choices counts against it.

Which specific conclusion about the RBOHC-associated cadmium response would need to change for a difference in magnitude to matter?

Yes, I'd prespecify a tolerance on the absolute difference between RBOHC log fold changes across normalization methods, using a fixed log base, though we haven't established a defensible numerical cutoff.

For the group contrasts, what difference in log fold change across normalization methods would you count as small enough to call them preserved?

Suppose normalization only rescales observed values and leaves detection calls fixed. Any change in detection rates within abundance bins would then reflect proteins moving between bins. For that comparison, I’d keep bin membership fixed so reassignment isn’t mistaken for changed detection.

I'd specify an acceptable change in contrast magnitude before comparing normalization choices. Suppose an RBOHC-associated contrast keeps its direction but its estimated log fold change halves under another normalization: that would support agreement in direction, while leaving the size of the response sensitive to scaling.

There are at least two claims hiding inside “sensitive”: that the direction of each secretion system contrast stays the same, and that its magnitude remains comparable after scaling. A protein could keep its direction while its effect size or detection status changes enough to alter the biological interpretation. Which result is the claim meant to preserve: sign, effect size, detection, or the ranked set of secreted substrates?

The comparison can test whether interaction rankings survive plausible scaling choices, but it cannot identify localization as the cause. A candidate interaction is weakened if its direction changes across defensible bait-recovery and compartment-specific normalizations, especially when that instability tracks variant-specific missingness.