Washing scaling of GeneChip microarray expression

Background: Post-hybridization washing is an essential part of microarray experiments. Both the quality of the experimental washing protocol and adequate consideration of washing in intensity calibration ultimately affect the quality of the expression estimates extracted from the microarray intensities. Results: We conducted experiments on GeneChip microarrays with altered protocols for washing, scanning and staining to study the probe-level intensity changes as a function of the number of washing cycles. For calibration and analysis of the intensity data we make use of the ‘hook’ method which allows intensity contributions due to non-specific and specific hybridization of perfect match (PM) and mismatch (MM) probes to be disentangled in a sequence specific manner. On average, washing according to the standard protocol removes about 90% of the non-specific background and about 30-50% and less than 10% of the specific targets from the MM and PM, respectively. Analysis of the washin...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Hans Binder, Knut Krohn, Conrad J. Burden
• Keywords: BMCBI 2007, BMCBI 2010, Intensity Contribution, Stringent Washing Cycles, Washing Function