[R] Estimating correlation in multiple measures data

[Michal Figurski]

Dear R-helpers,

This may sound simple to you, but I'm a beginner in this, so please be 
forgiving.
I have a following problem: two analytes were measured in patient's 
blood on 4 occasions: ProteinA and ProteinB. How to correctly evaluate 
correlation between ProteinA and ProteinB?

I tried:
x <- data.frame(Patient.ID=rep(1:10, each=4), Visit=rep(c(1:4),10), 
ProteinA=rnorm(m=10, n=40), ProteinB=rnorm(m=13,s=0.7,n=40))

gls(ProteinB~ProteinA, data=x, corr=corSymm(form=~Visit|Patient.ID)

In the results I see correlations between the occasions and between 
terms, but not between the proteins. Where to look for it?

-- 
Michal J. Figurski, PhD
HUP, Pathology & Laboratory Medicine
Biomarker Research Laboratory
3400 Spruce St. 7 Maloney S
Philadelphia, PA 19104
tel. (215) 662-3413