How to association the methylation profiling with the expression? - statistic questions about the bisulfite sequencing (Jul/18/2007 )

I have worked on the methylation profiling of gene promoter using bisulfite sequencing and have got one 400bp fragment of converted sequence. The C to T conversion rates in CpG are that I am interested in. Some of the C in CpG 100% converted to T,but some are not, the converted rates of C to T are 0-100%,totally quantitative and continuous,not the ideal 0 and 1. Then the question comes out: How to calulate/value the C to T conversion rates in specific CpG since the value of conversion rates are continuous? Next,since the conversion rates is continuous,then what kind of statistic should I do to relate the methylation profiling to the expression or diease phenotype?
Thanks for any kind of help!

You did direct sequencing, I presume? Than you can roughly calculate the amount of methylation by the formula %=100*C/(C+T) with C and T representing the peak height at every CpG. With the % methylation value you can do normal statistics like group comparisons, correlation or regression.