I’ve been working on extracting the clusters out from my heatmap and finally succeeded with this R script!
|Mean Protein Abundance||181.025||168.728||284.94||301.742|
distfun = function(x) as.dist(1 - cor(t(x), use = "pa"))
Question: Should I get error rates for the mean protein abundance of each cluster and silo?
I’m currently working on doing the same thing with the ASCA temperature influenced proteins (the ASCA table requires some different reformatting).
I had a lot of trouble trying to make a venn diagram in R (here is my attempt…). I did use the previous script to sort out a list of the proteins in each temperature, but ultimately I decided to refer back to Emma’s paper (2) and use Venny (2) the same way she did.
(1) Oliveros, J. C. Venny. An interactive tool for comparing lists with Venn’s diagrams.
https://bioinfogp.cnb.csic.es/tools/venny/index.html (accessed February 13, 2019).
(2) Timmins-Schiffman, E. B., Crandall, G. A., Vadopalas, B., Riffle, M. E., Nunn, B. L., Roberts, S. B. (2017). Integrating Discovery-driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation. Journal of Proteome Research, 16(9), 3298–3309.doi:10.1021/acs.jproteome.7b00288.