I merged the Uniprot annotated table with each silo that had the quantitative and qualitative tags I previously made: new table .
I want to note this table includes proteins that are not abundant in each silo. I choose to include this for now since they are easily removable. I was thinking that some Revigo plots with the 0 abundance proteins might reveal some differences between the silos… There is ~1000 to 1500 proteins not expressed in each table (out of about 8400 proteins).
I’m making a new scree plot since my last scree plots weren’t with the right code (nhclus.scree(x, max.k=#)), however it has not been successful yet because of the amount of time it’s taking. I’ve let it run over 4 hours with no results produced. I am trying it one more time and am planning on letting it run overnight, however if it takes that long it may not be feasible since I need to do it 3 times and then run kmeans which takes a few hours itself…
Also, this came up lab meeting: changing max.print options in R .