Sources of high variance between probe signals in Affymetrix short oligonucleotide microarrays.

ABSTRACT: 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 tar

SUBMITTER: Jaksik R 

PROVIDER: S-EPMC3926573 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature