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| Research article summary (published 30 Dec 2001): |
Improved background correction for spotted DNA microarrays.
Full Abstract
Most microarray scanning software for glass spotted arrays provides estimates for the intensity for the "foreground" and "background" of two channels for every spot. The common approach in further analyzing such data is to first subtract the background from the foreground for each channel and to use the ratio of these two results as the estimate of the expression level. The resulting ratios are, after possible averaging over replicates, the usual inputs for further data analysis, such as clustering. If, with this background correction procedure, the foreground intensity was smaller than the background intensity for a channel, that spot (on that array) yields no usable data. In this paper it is argued that this preprocessing leads to estimates of the expression that have a much larger variance than needed when the expression levels are low.
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Author information
Author/s: Kooperberg, Charles (C); Fazzio, Thomas G (TG); Delrow, Jeffrey J (JJ); Tsukiyama, Toshio (T);
Affiliation: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, MP 1002, Seattle, WA 98109-1024, USA. clk(-atsign-)fhcr.org.
Grants: CA 74841 (Agency:United States NCI) ; GM58465 (Agency:United States NIGMS)
Journal and publication information
Publication Type: Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.
Journal: Journal of computational biology : a journal of computational molecular cell biology (J Comput Biol), published in United States. (Language: eng)
Reference: 2002-; vol 9 (issue 1) : pp 55-66
Dates: Created 2002/03/25; Completed 2002/06/24; Revised 2007/11/14;
PMID: 11911795, status: MEDLINE (last retrieval date: 11/6/2008)
Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.
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