I'm looking to do a PCA analysis on count based data itself rather than averages. I'm hoping this will help for variable observation depths; for example, 3/4 reads is not really equivalent to 15/20. There is more confidence in the 15/20 being near 75% than for the 3/4.
Any ideas how how I could do this?
Here is some example data, each site is the number of positive reads and the number of total reads.
Individual, Site1, Site 2, ... Indiv1, 7/9, 4/5, ... Indiv2, 5/11, 7/22, ... Indiv3, 14/29, 3/5, ...