5.8 years ago by
Maastricht, The Netherlands
I would think that PCA for proteomics is in fact a lot simpler than for SNP data. SNPRelate does a lot of pretreatment steps that are not needed assuming you have proteomics results (as in amounts of individual proteins with some identifier even if that is just a spot location for different conditions. Unless I am wrong that means you can just do basic PCA for R. See e.g. here. There are a number of "easy to use" packages out there. If that is what you are looking for just Google for "Principal Component Analysis in R"