Kaitlyn’s Notebook: NMDS and Protein Quant

Just a refresher, I’ve been working with Rhonda’s 2016 oyster larvae data.

This experiment looked at oyster mortality based on two temperatures: 23C and 29C. Proteomic work was done on 3 silos, two at 23C and one at 29C.  When the data between Silo 2 and Silo 3 is compared, we can see that Silo 2 had higher rates of mortality.  Silo 3 and 9, which were at 23C and 29C respectively, had the same mortality rate of 10%. Therefore we decided to make an NMDS that looked at Silo 3 and 9 only. The X is an artifact of the code. The First number is the silo number and the number following the underscore is the day of the experiment.

It looks like Silo 3 had more days that were less similar to most days of the experiment. Silo 3 was at 23C. Rhonda previously reported that hatcheries are growing larvae at 29C because of the higher mortality rate that occurs at 23C. This NMDS plot shows that the beginning of the experiment (day 3) and the end of the experiment (day 15), silo 3 stood out. Silo 9 seems more consistently related to other days of the experiment.

For comparison, here is the previous NMDS plot containing all of the silos:

In addition to the NMDS, I did a quick quantification of the different proteins expressed each day (under “Protein”) and the total protein abundance (under “Protein Abundance”).