R Help is Helpful

Using the help pages for ordiplot, I was able to modify my code and make a better NMDS plot:

ordiplot(proc.nmds.euclidean, choices = c(1,2), type = "text", display = "sites") #Plot refined NMDS displaying only samples with their names

• choices: Specify which axes you want to display
• type: What you want displayed. Instead of “points,” using “text” allows me to display the row and column names
• display: There are two options: sites and species. In the previous NMDS plot, sites are the white dots and species are the red crosshairs. Sites relate to my columns, which are my samples. Therefore, I only want to display sites.

I was unsure about whether or not to include PRTC peptides in my technical replicate cluster analysis. Yesterday I removed the PRTC peptides, which lead me to a plot that looks like this:

Figure 1. NMDS using euclidean distances and untransformed data without PRTC peptides.

Adding the peptides back in, I get a different cluster pattern:

Figure 2. NMDS using euclidean distances and untransformed data with PRTC peptides.

For both plots, it looks like there is variation that needs to be normalized before I reexamine my data. I emailed Emma, who said I should not use PRTC peptides. I saved the NMDS plot here. She also said I should normalize my data with TIC content. I need to go through my RAW files and get the TIC content so I can continue analyzing data. However, we need the program xcalibur to open up RAW files. It’s not installed on Woodpecker, but Emma has access to it. I will see if I can access a Genome Sciences computer and look at my RAW files.