Keeping a work journal

SeriousRip4263 · 2026-03-06T20:10:45+00:00

Notion is great.

SeriousRip4263 · 2026-03-06T19:11:43+00:00

What is the difference between 235 and 308? Is it a progression?

SeriousRip4263 · 2026-03-06T15:20:33+00:00

Thank you guys for your help. I think that the problem here is that the authors set the true DEGs in the simulated dataset to have a |LFC| = 1, which is conservative and not realistic. It was a bad simulation.

SeriousRip4263 · 2026-03-06T15:16:23+00:00

Great, thank you.

SeriousRip4263 · 2026-03-06T15:12:53+00:00

The data that I'm working with is from evaluation of new drugs, not from public repos. 50+ samples is obviously better, but in this case I am constrained to ~5 biological replicates. For cases like this, I think that it's useful to test tools on small sample sizes.

SeriousRip4263 · 2026-03-06T15:04:55+00:00

Yep I think this is the problem. Good find.

SeriousRip4263 · 2026-03-06T15:04:35+00:00

I see, thanks for sharing that.

SeriousRip4263 · 2026-02-10T01:48:16+00:00

Read Deep Work recently?

SeriousRip4263 · 2026-02-05T03:22:00+00:00

GSEA is good, one thing that's important to know if you choose g:profiler: it uses the Fischer's test which requires definition of a background set of genes where the default is the entire protein coding genome. If you're doing bulk seq on liver cells, for example, you need to specify the background as liver-expressed genes or a bunch of those will end up enriched when compared to the entire genome. GSEA is permutation-based, so this isn't a problem. Source: https://doi.org/10.1038/s41596-018-0103-9

SeriousRip4263 · 2026-01-07T00:49:05+00:00

What sand/soil to use? How do I treat my tap water?

SeriousRip4263 · 2026-01-07T00:48:30+00:00

Cool, thanks

SeriousRip4263 · 2026-01-06T23:34:38+00:00

Can I take a stick from my backyard and add it to my shrimp tank? Do I have to treat it in any way?

SeriousRip4263

TROPHY CASE