[R] about 2 color variance stabilization

[=?gb2312?B?w8/QwA==?=]

Hello sir:
A paper of you named"Exact and Approximate Variance-Stabilizing Transformations for Two-Color Microarrays" is very helpful for my work.
A question which needs your help.Thanks a lot.
For instance,cy3~control  cy5~treatment
And after calculating the "h"transformation for each channel,we can get h(cy3) and h(cy5).But obviously,each h value isn't calculated individually ,but through the information of the all 2 channels.I wanna know how the "all 2 channels"'s information is included in h transformation.
By using the "vsn"package under R environment,if I enter only 1 channel(i.e. just 1 column data for gene expression),the system gives warning which notice me that I must enter at least 2 channels(i.e. 2 column data for gene expression).If I enter to channel,I can get the h value for each of the 2 channels.So I wanna know how to use the "all 2 channels"'s imformation for the h transformation.
Thanks again.
 
My best regards!