[R] about vsn

=?gb2312?B?w8/QwA==?= xmeng at capitalbio.com
Mon Dec 13 03:10:51 CET 2004

Hello sir:
As to the "variance stabilization" method which is applied in the "vsn"package under R environment,here's a question about the ratio of the 2 channels:
After applying vsn,we can get new_cy5 and new_cy3 intensity according to the original cy5 and cy3 intensity respectively. And the new_cy5 new_cy3 are similar with ln(intensity).

But how can I calculate the ratio=cy5/cy3 ?

If the new_cy5 and new_cy3 is log2(intensity),the ratio equals  to 2^(log2cy5-log2cy3),but as to vsn,how to get the ratio?
Since the vsn transformation is similar to ln transformation when the intensity is high, I wanna know how high the intensity is so that I can use ln instead of vsn?

Thanks a lot!

my best regards!

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