Estimating robustness of the tileShuffle method with repeated probes

Motivation: In this paper the TileShuffle method is evaluated as a search method for candidate lncRNAs at 8q24.2. The method is run on three microarrays. Microarrays which all contained the same sample and repeated copies of tiled probes. This allows the coherence of the selection method within and between microarrays to be estimated by Monte Carlo simulations on the repeated probes. Results: The results show poor consistency in areas selected between arrays containing identical samples. A crude application of the method can result in majority of the region to be selected, resulting in a need for further restrictions on the selection. Restrictions based on ranking internal tileShuffle test statistics do not increase precision. As the tileShuffle method has been shown to have higher precision than the MAS and TAS software, one can conclude that methods giving unreliable results are in common use. University of Iceland, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland deCODE Genetics, Sturlugata 8, 101 Reykjavik, Iceland. to whom correspondence should be addressed