Cy3 vs Cy5 - (Dec/09/2005 )

Hi, I'm new to microarray business.
I'm going to label some fragmented genomic DNA samples with Cy3 and Cy5 dyes using the random-prime method.
I read somewhere that Cy3 gets incorporated to the probe quite a bit more efficiently than Cy5. Is this generally true?
Also, if given the same level of incorporation, are Cy3 and Cy5 of the same intensity?

yes, this is true and very common.
What we call this is dye-swap.

I have read several publications that Alexa Fluor Dyes does not have much swap as Cy dyes, and the signal intensity is higher.
Alexa Fluor 555 and Alexa Fluor 647 dyes provide higher confidence than Cy3 and Cy5 dyes in determining significant differences in gene expression on microarrays
http://probes.invitrogen.com/servlets/posters?id=291