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In translational profiling polysomal and subpolysomal mRNA fractions are analysed on the same chip to allow any changes in ratio between these two states to be monitored. Microarray processing methods usually assume that deregulation occurs in a low proportion of genes and in equal symmetry of upregulation and downregulation;  translatome studies violate these assumptions. We provide the analytical background and support for translational profiling studies using in-house developed and freely available pipelines.