I don't think you can say that Naviaux findings are all due to inactivity, it sounds to simplistic. If we take sphingolipids for example; we see in metabolic syndrome (inactive) patiënts that sphingolipids are usually high, not low like in ME/CFS patiënts.
It is important to exclude simple explanations before moving on to more speculative ones. I would guess that sphingolipids in plasma derive from damaged cell membranes. I doubt they are synthesised and exported to be used in other cells. People with metabolic syndrome may be relatively inactive but they have lots of reasons for damaging cells. Many are overweight and so will have more daily muscle damage simply from carrying that weight around. Many have high glucose levels, which damages cells. Hypertension also damages cells. And of course they have abnormal lipid handling anyway. So there are lots of reasons for them not having low sphingolipid even if inactivity lowers sphingolipid if all other factors are equal. (Much the same applies to femoral osteopenia, which occurs with inactivity but not in obese people who load the femur at high rates.)
I've wondered about medicine looking at single variables in the past. I've done quite a bit of work on classification where you need to take multiple variables to get a decent signal. Sometimes it is because of noise. But I've been looking a bit at anomaly detection recently and I think multivariate data here is good because you have one or multiple normal clusters from a multivariate vector then anomalies may deviate from these in many ways.
You may be right. But there is something that does not quite fit for me here. If this is a question of a heterogeneous mix of overlapping pathway shifts then it is extremely unlikely that any replicable formula based on MVA will identify 94-96% of cases correctly. As you know you can always produce a formula that will identify a group this precisely within a cohort but if things are very heterogeneous then almost by definition this is going to be a non-replicable formula.
In conditions like RA we have never got near a formula that identifies 95% of cases correctly. In at least 10% of cases all physicians will say that are not really sure if it is RA anyway.
I would be much more impressed if a formula of three factors picked out 60% of ME/CFS patients and 10% of controls, for instance. The trouble with the current trend for presenting statistically pre-digested data is that we never see the original scatter plots.
Of course hidden behind the 96% score may be exactly such a 60/10 split for some major variables and it may pan out as something of key importance. Maybe we need a friendly FOI request for the raw data!
More to the point a rapid re-run with another blinded controlled cohort like the UK Biobank could turn this from a maybe into a racing certainty.