[BioC] Spot with high ratio but low cy3?

[Cheng, Meng-Chuan]

Hi!

I am analyzing a data set that is background corrected and normalized using MA method.
I got a list of spots that have high M value which I am interested in studying.
But the list also includes some spots that have high logratio(M) due to the small value of Cy3, which i am not interested in. For example, if Cy5=24 and Cy3=0.8, then my ratio is 30. Those spots would be in the up-regulated list but, in fact, their expression is pretty low.
Is there any way or any package in bioconductor I can use so that I can screen those spots with small cy3 value out?

Best,

Meng Cheng