Hi! I have a couple of qustions about PCA plots for microarrays. I have run a number of affymetrix arrays, and used the affy package for background correction, normalization etc (standard RMA procedure). When I then want to make PCA plot of the arrays, what makes most sense: To use the values from rma which are log scale, or to transform them back to "normal scale"? (In my case the latter gives more outliers...). Is there any established standard for doing this?

kind regards
Jakub Orzechowski 
	[[alternative HTML version deleted]]

