I have set of genes for which we want to make sure that these are translating in order to proceed for next step of the experiment. I got few ribosomal profiling datasets for my species (all are microarray except one). If I am not wrong then I should check the intensity values of my genes from the microarray dataset in order to say that set of my genes with intensity above a threshold are translating. Can any one please let me know what would the stringency criteria in this case.
Is there any tool/package for this work? Guidelines to start analyzing these datsets or recommendation of some good papers would also be helpful.
Many thanks, R.