Jack

Hi @igrabski , I can't see anything, but I'm wondering if this has been solved? I'm having a similar issue where running JoinLayers() on 50 samples is taking an age...

Hi, Things run fine in smaller sample sizes, and I can't share the full dataset unfortunately. I'll try and find a public dataset to replicate the issue. I've ran a...

> * [ ] Perform all calculations in sparse matrices (or hdf5) to avoid the computer collapsing because of RAM requirements. @jgarces02 I'll look at doing this when I get...

Hi @tuhulab Sorry for the late reply. Appreciate the comments. This is a tough one because ideally, if the clustering is granular enough, downsampling the cells shouldn't have a large...

Hi, If you run `?compare_pathways` there's some more explanation on this: > Value Statistical results from the SCPA analysis. The qval should be the primary metric that is used to...

Yup, that's right. A negative fold case in your situation would mean higher in healthy (or lower in hiv). I would pay more attention to the qval and adjusted pvalue...

Hi. It looks like you're only supplying one population in `marrow`. You need to supply 2 or more populations for the comparison to run. Jack

Can you give me the code you're using to generate the blood and marrow objects?

Hi, Sorry for the delay in getting back to you. Maybe we should be more explicit in the documentation here, but we're assuming that the data used as input into...

Yup, the higher the fold change, the more the pathway will be enriched. The one caveat here is there there isn't a normalisation to pathway size, so pathways with larger...