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Some discussion has been moved to: Deconditioning – relevance and irrelevance

Oh yeah, none of my posts were specifically about the method in the present paper. Just pushing back specifically on saying someone was probably misdiagnosed if we did find a robust rare variant connection. Edit: Which I am now thinking might not have been Utsikt's point anyway.

Honestly, my statement was just based on the abstracts (there's two links btw). It was just to make the point that researchers can and do talk about mixtures of different rare and common variants as being causal for the same disease. Edit: So in answer to your question, I'm not sure of the...

Some of the references seem to be numbered wrong, since these seem unrelated to the sentences:

Immunological Density Shapes Recovery Trajectories in Long COVID [Line breaks added] Abstract Post-acute sequelae of SARS-CoV-2 infection (Long COVID) frequently persists for months, yet drivers of clinical remission remain incompletely defined. Here we analyzed 97,564 longitudinal PASC...

Just to cover all the bases..were the groups mixed up for all the measurement steps? So the order of testing would be something like HC, HC, ME, HC, ME, ME, HC, ME, ME, HC. Or was any step more like all the HCs go first, then the ME/CFS samples got tested next, even if right after? Just to rule...

That figure is really quite striking. From the stats in the supplementary files, it doesn't look like any other lipid came close. q=.0017 and FC=0.32 for this lipid versus q=0.79 and FC=0.64 for the next most significant one (PE(O-40:5)). I haven't had a chance to really study the methods (and...

I don't know if it's common practice or not - I'm pretty sure I've seen volcano plots where the significance line showed the cutoff of adjusted values (though I also found several that use .05 for the cutoff line just now, like you said). Either way, I don't think you need to show where .05 is...

Discussion about optimal plotting methods has been moved to a new thread: Data visualization

Maybe I'm coming around. This one is kind of aesthetically pleasing and easy to interpret.

It seems to be the same thing in many papers from this group. Disclaimer that I haven't read all these in detail so I might have missed something, but it looks to me like they all might be using tests which assume independence but are comparing multiple cells per person. For example, from the...

Were the adjusted p-values used in the paper? I see that there are FDR values in table S2 for the pathways, in which only vitamin B6 metabolism is below .05. But the text and figure 1A seem to be based on the raw p-values.

Oh okay, I thought you were mainly aiming for the binning aspect, not necessarily keeping it asymmetrical like a standard histogram.

Oh I understand. Basically bin them to the width of one of the circles. Yeah, I mean like here's a paper where after they corrected an error in their plot, they switched to the binned dot plot/histogram type visualization. I like the exact values on the left better. Edit: But I can see an...

I'm not sure what you mean by round to the nearest point. Is it difficult to compare groups in the plot I shared? Along with an overlaid median line and maybe box plot, it seems to be good to see differences in distribution. I guess a histogram looks a little less visually messy.

It's basically the same thing except the exact value can be shown in a swarm plot, instead of being put in bins of arbitrary width in a histogram. But swarm plots where the points are overlapping, like in this paper, don't seem as helpful because you can't see the distribution clearly.

The Groton Maze Learning task seemed to produce the largest differences in this study. A while ago, I wanted to see if I might be able to do the task myself somehow on a regular basis to track cognition. I couldn't find any sources where it was freely available, so I tried to piece the...

Yeah, I like that idea. Any idea why the digit span plot doesn't include the more recent MCAM study (Lange 2024)? I haven't looked at it in a while, but it was pretty large and seems to have included backwards digit span tests which were non-significant.

Thanks @ME/CFS Science Blog for the quick summary on Bluesky. The nearly consistent direction of effect in the plots is interesting.

My guess is that all the points with identical values were below the limit of detection, and were just given an abitrary low value. That might be what this sentence is talking about: Edit: Though that doesn't explain why some points are also below this value, and one is even at 0.