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Sensors 2014, 14(1), 532-548; doi:10.3390/s140100532

Sources of High Variance between Probe Signals in Affymetrix Short Oligonucleotide Microarrays

1,* , 2
Received: 15 October 2013 / Revised: 16 December 2013 / Accepted: 24 December 2013 / Published: 31 December 2013
(This article belongs to the Special Issue Microarray Sensors)
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High density oligonucleotide microarrays present a big challenge for statistical data processing methods which aim to separate changes induced by experimental factors from those caused by artifacts and measurement inaccuracies. Despite huge advances in the field of microarray probe design methods, the signal variation between probes that target a single transcript is substantially larger than their between-replicate array variability, suggesting a large influence of various probe-specific effects that introduce bias to the data. In this work we present the influence of probe-related design variations on the expression intensities of individual probes, focusing on five potential sources of high probe signal variance: the GC composition of the probe, the distance between individual probe target sites, G-quadruplex formation in the probe sequence, the occurrence of sequence motifs complementary to the oligo(dT) primer, and the specificity of unrecognized alternative splicing probeset assignment. By focusing on two high quality microarray datasets based on two distinct array designs we show the extent of variance between probes that target a specific transcript providing guidelines for the future design of microarrays and data processing methods.
Keywords: microarrays; GC-content; custom CDF; G-quadruplex; oligo(dT) microarrays; GC-content; custom CDF; G-quadruplex; oligo(dT)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Jaksik, R.; Marczyk, M.; Polanska, J.; Rzeszowska-Wolny, J. Sources of High Variance between Probe Signals in Affymetrix Short Oligonucleotide Microarrays. Sensors 2014, 14, 532-548.

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