Figuring Out WGCNA, Part 2

Recap Alright, so last time, I hit a wall with memory allocation when attempting to analyze ambient-temperature crabs. At first, I tried to get around this issue by just heading into UW and using the computers there. That partially solved the issue, but not entirely. At one stage in the pipeline, you set a bar that determines what genes should be discarded – the original recommendation is genes where counts are below 10 in 90% of samples, but since I had only 9 samples, just changed it to counts below 10 in all samples. Problem: that crashes the lab computers entirely, and even upping the bar to 15 takes practically an entire day to run. So as an alternative, I started using RStudio on Mox, following the guidelines figured out here. That partially worked, but it still takes a really long time to run 10 samples, so I decided to…

from Aidan F. Coyle