Exploration of probes selection criteria of oligonucleotide array

Abstract

Microarray experiments allow us to study the expression patterns of thousands of genes simultaneously and observe the interaction among genes when they are put under the same experimental conditions. A few preprocessing methods have been proposed in the recent years with the objective of improving the gene expression measures. These methods make use of all the probe pairs of every gene in their estimations.Most of the probe pairs selected to be on the probe array are generally about 600bp (base pair) from then 3a?? end due to labelling efficiency which is more optimal within this distance. However, there are some probe pairs that are more than 600bp from the 3a?? end. Thus, in this report we will make use of the existing method: robust multiarray average (RMA) to explore a few distances (1000, 800, and 600bp) to identify a threshold. This cut off will determine probe pairs that are considered far from 3a?? end but without losing too much information when estimating the gene expression measures.