SRM Analysis Part 4
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.