I'm a biochem guy so the stats in this paper are giving me a real hard time.
Kliman, RM, Irving, N, and Santiago, M. Selection Conflicts, Gene Expression, and Codon Usage Trends in Yeast. J Mol Evol (2003) 57:98–109 (PDF copy)
In this paper I'm having a hard time figuring out exactly what they did to find factors 1&2. On page 3, paragraph 4 they give only the briefest of explanations. They use the frequencies of synonymous codons for each AA class and mysteriously enter these values into factor analysis. What exactly does this statement mean?