Use dual channel as 1 channel
 

Hi guys, I am a bachelor student and I need some help with microarray.
I want to create a small database about gene expression of a plant in physeological condition. I have a lot of dual channel experiments, with Cy3 channel exploited to check several stress and Cy5 used as control. Can I consider only the Cy5 light measures of the dual channel array to make average and obtain the physeological expression values? Thanks in advance.