Remaining Analyses

Squeezing every last bit of information out of my data

As I outlined in my November Goals, this week I’m playing around with my dataset to see if I can pool my eelgrass and bare samples, and repeating my NMDS and ANOSIM analyses. I know Steven said to focus on protein-level responses, but I’m curious…

Step 1: Rerun NMDS and ANOSIM without pooling


Site only ANOSIM: R = 0.01339, Significance: 0.326 Eelgrass/Bare only ANOSIM: R = 0.02932, Significance: 0.168 Site and eelgrass ANOSIM: R = 0.00386, Significance: 0.41

Nothing significant, but here’s the pattern I see in that NMDS:


Figure 1. Annotated NMDS plot

My groups overlap because there’s still a lot of variability within my groups. This could be due to the alternative splicing I’m seeing within my protein abundances.

Step 2: Pool eelgrass and bare samples

There has been no indication that my eelgrass samples have significantly different protein expression results from my bare samples (see above eelgrass-only ANOSIM results). So I pooled them. Again nothing significant, but it’s nice looking at a less-distracting picture.


ANOSIM: R = 0.01339, Significance: 0.321


Figure 2. Annotated NMDS plot after pooling bare and eelgrass samples

I’m just go ahead and say we’re about done here. No more NMDS and ANOSIMs!

Written on November 1, 2017