Sources of nonlinearity in cDNA microarray expression measurements 英文参考文献.docVIP

/2001/2/11/research/0047.1 Research Sources of nonlinearity in cDNA microarray expression measurements Latha Ramdas*, Kevin R Coombes??, Keith Baggerly?, Lynne Abruzzo§, W Edward Highsmith?, Tammy Krogmann?, Stanley R Hamilton* and Wei Zhang* Addresses: *Departments of Pathology, ?Biostatistics, ?Biomathematics and §Hematopathology, Cancer Genomics Core Laboratory, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA. ?Department of Pathology, University of Maryland, College Park, MD 20742, USA. Correspondence: Wei Zhang. E-mail: wzhang@ Published: 18 October 2001 Received: 23 July 2001 Revised: 30 August 2001 Accepted: 11 September 2001 GenomeBiology 2001, 2(11):research0047.1–0047.7 The electronic version of this article is the complete one and can be found online at /2001/2/11/research/0047 ? 2001 Ramdas et al., licensee BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) Abstract Background: A key assumption in the analysis of microarray data is that the quantified signal intensities are linearly related to the expression levels of the corresponding genes. To test this assumption, we experimentally examined the relationship between signal and expression for the two types of microarrays we most commonly encounter: radioactively labeled cDNAs on nylon membranes and fluorescently labeled cDNAs on glass slides. Results: We uncovered two sources of nonlinearity. The first, which led to discrepancies in analysis affecting the fluorescent signals, was signal quenching associated with excessive dye concentrations. The second, affecting the radioactive signals, was a nonlinear transformation of the raw data introduced by the scanner. Correction for this transformation was made by some, but not all, image-quantification software packages. Conclusions: The second type of nonlinearity is more troublesome, because it could not have been predicted a priori. Both types of nonli