Shelly’s Notebook: Fri. Jan 17, 2019, Oyster Seed Proteomics to explain mortality

I took a quick look at Silo 2 vs Silo 3 proteomes because silo 2 had 2% survival where silo 3 had 10% survival.

1f9a5bf8-a65e-11e6-9342-30300e6de4db.png graph is from here

PCA of silo 2 and 3 technical replicates looked good so averaged the NSAF values. unnamed-chunk-9-1.png

Here’s the heatmap of silo 2 vs silo 3. avgNSAF_siloEffect_cutoff0.025_heatmap_OrderedBysilo_ShortNames-1.png

Day 11 and 13 show stark differences in silo 2 compared to silo 3. The top cluster of proteins show very high expression and the bottom cluster show very low expression in silo 2 compared to silo 3.

Need to look into what these proteins are

Markdown files:
generated by these R markdown files: ASCA_avgNSAFvals_AllProteins_Silo2v3.Rmd and ClusteringTechnicalReplicatesSilo2vs3.Rmd.

from shellytrigg