I was waiting to get a reply from someone at mapMECFS to see if it would be okay for me to still post the data I previously analyzed, and I was told I could.
I see it's already been mostly discussed at length, but they also suggested I note that there may be reasons for the differences, such as duration of illness, and the fact that cortisol fluctuates throughout the day, and possibly even changes significantly after death.
But here is the cortisol CSF data from the deep phenotyping study. There appears to be virtually no difference between the groups.
One note is that I have some concerns that there might have been some sort of issue with the CSF metabolomics part of the deep phenotyping study, as nearly all of the 435 metabolites (88%) were lower in ME/CFS. I posted about it on
PubPeer. Although if metabolites were biased lower, presumably that would make a true low cortisol finding look even more significant, not less.
Edit: When comparing these groups with a Mann-Whitney test, p=0.467.