WGCNA Part 3

Success!! So last time I ran WGCNA, I was running it solely on individual groups of crabs (i.e. all elevated-temp or ambient-temp crabs over time), examining solely the effects of day rather than temperature. However, that isn’t really the best way to use WGCNA – it can look at correlation to multiple variables simultaneously. So I decided to go back and look at two more comparisons of libraries over time! All of these comparisons were performed on libraries aligned to our three main transcriptomes – cbai_transcriptomev2.0 (unfiltered by taxa), cbai_transcriptomev4.0 (filtered to only include presumed Chionoecetes sequences), and hemat_transcriptomev1.6 (filtered to only include presumed Alveolata sequences). Furthermore, each comparison included variables for day (0, 2, 17), temperature (elevated, ambient, lowered), infection status if relevant (infected, uninfected), and crab ID. First comparison: Ambient and Elevated-temperature crab (Ambient vs. Elevated). For this, all available time points for crabs A-C (ambient-temp treatment group)…

from Aidan F. Coyle https://ift.tt/3wHw7sj