Survey of background normalisation in affymetrix arrays and a case study

Abstract

The oligonucleotide is a special type of one-channel microarrays which has 25-base pair long and the Affymetrix is the well-known oligonucleotide. In this study the normalisation procedure which enables us to discard the systematic erroneous signals in the measurements is described. Then different gene expression indices which are used to compute the true signals via the background normalisation are described in details. In these descriptions two recently suggested alternative approaches, namely frequentist (FGX) and robust (RGX) gene expression indices are explained besides the well-known approaches in this field. Finally a comparative analysis of the real microarray data with different sizes is presented to evaluate the performance of the underlying methods with RMA which is one of the common techniques in the analysis of microarray studies. © 2012 Springer Berlin Heidelberg.