Organising data for confidence intervals

Hi all,

I need to calculate confidence intervals for some parameters i estimated. i did a global partameter estimation and so got 8 parameters. i have 7 data and the 7 seven corresponding simulated sets and three experiments. each experiment has its own sets with differing numbers of discrete time points. i need to build a covarience matrix in order to get the confidence intervals.

anyone know how i can arrange my data to do this?