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