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No, I know, I mean a difference that is obscured by correcting for osmolarity (which means there wouldnt be a good way to detect changes anyways if there was a big between-group osmolarity difference—I’ll try to check that from their public data as well) [edit: I’ve had similar issues trying to...

As far as I remember, this wasnt a finding that was mirrored in the plasma studies from the same participants (I will try to go back and double check later today if I have time). Which makes me think it might have something to do with osmolarity in urine samples. I remember some folks on the...

Ah okay I missed delta there, thanks for pointing it out. So really just an interpretational issue for what no significant mean change within group could mean biologically

Variance was perhaps the wrong word to use, what would matter is directional variability between timepoints. Because in the control plots shown there is similar spread but also all trend upward, which drives a mean difference despite similar SD within the before and after data points. Does that...

Good to hear, hopefully it was the same in the ME/CFS publication

When the lack of significant metabolites after exercise is referred to as “striking” and interpreted in the abstract and text as potential evidence of a failure to adapt after exercise (and “anomalous recovery” in the title), I think it is incompatible with the data just showing much more [edit...

Do you mean individually or collectively? I see quite a few instances where the ME/CFS lines have a noticeable slope, even on par with the control lines in many cases (though often in the opposite direction). [Edit: I think it becomes necessary to look at individual slopes because “levels change...

Okay so agree with the critiques already raised earlier in this thread. Basically the major problem that’s happening here is data leakage. First, it looks like the data pre-processing was all done together for all “train” and “test” splits in the CV, which already introduces bleed with...

Ah my bad, [edit: I was jumping between tabs and] I thought this was the thread for the presentation conference. That’s not a true independent test set, theyre only reporting the effects of training the model essentially 5 times, not how an internally cross validated trained model performs on...

Wait a minute I have to check the numbers on the original paper. They say it’s a 20% test split from 98 samples, but in their confusion matrix they have instances of 1% of the cohort being misclassified in a particular way, which would be 0.2 of a person. Also their workflow diagram seems to...

I went back to the 2023 ME/CFS Raman spectroscopy paper to see if that might clarify and it just made me more confused—it looks like they sorted individual cells and then averaged them per patient. I am not sure if that would be analogous to the “single cell” or “patient level” measurement here...

I assume it’s the difference between individually classifying the spectra of single cells (multiple cases per participant treated separately) vs. pooling multiple cells per participant. I would guess the latter is probably being confounded by a difference in cell frequencies, same as other...

Theoretically it might! Or, rather, I’m thinking it might be more of a hint to the upstream problem.

There have been several metabolomics studies where glucose was detectable—one or two found just slightly higher glucose compared to controls (still well below even pre-diabetes range, iirc), and several other studies did not replicate this. If anything it might be a comorbidity that comes up...

They’re pretty multi-purpose enzymes used in a bunch of endogenous processes like steroid synthesis. It’s mostly that they handle several fundamental chemical conversions for compounds that traffic through the liver (which ends up including a lot of things in the circulation) and those...

Yeah I think this method is going to be extraordinarily prone to overfitting if you can’t even differentiate out individual features for feature selection, and is substantially less interpretable than other big data methods on a biological level.

I don’t know off the top of my head. Insulin resistance doesn’t seem to be a feature of ME/CFS at large, though.

Yes I've seen it, it seems like worsened symptoms afterwards was the most common response, though some people anecdotally also reported feeling drunk at lower amounts. My first paper in ME/CFS was also on that topic though it was a post-hoc analysis so I was very limited in the associations and...

Just some assorted thoughts after lectures in a drug development course got me thinking: There's a handful of enzymes that metabolize something like 80% of all small molecule drugs, so theoretically something that affects those enzymes could be expected to present exactly like this. The exact...

Realized belatedly that I forgot to post this with my other comments: These plots from figures 6 and 7 pretty much confirm it--there are definitely changes after exercise in the ME/CFS group, they're just all over the place so the mean difference isn't significant, [edit: or its too variable to...