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Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance.doc

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Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance

BMC Genomics BioMedCentral Research article Open Access Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance Vigdis Nygaard1, Anders L?land2, Marit Holden2, Mette Langaas2,3, H?vard Rue2,3, Fang Liu1, Ola Myklebost1, ?ystein Fodstad1, Eivind Hovig*1 and Birgitte Smith-S?rensen1 Address: 1Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway, 2Norwegian Computing Center, P.O. Box 114 Blindern, 0314 Oslo, Norway and 3Department of Mathematical Sciences, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway Email: Vigdis Nygaard - vigdisny@radium.uio.no; Anders L?land - Anders.Loland@nr.no; Marit Holden - Marit.Holden@nr.no; Mette Langaas - mettela@math.ntnu.no; H?vard Rue - hrue@stat.ntnu.no; Fang Liu - fangli@radium.uio.no; Ola Myklebost - olam@radium.uio.no; ?ystein Fodstad - fodstad@radium.uio.no; Eivind Hovig* - ehovig@radium.uio.no; Birgitte Smith- S?rensen - bss@radium.uio.no * Corresponding author Published: 23 March 2003 Received: 21 December 2002 Accepted: 23 March 2003 BMC Genomics 2003, 4:11 This article is available from: /1471-2164/4/11 ? 2003 Nygaard et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the articles original URL. mRNA amplificationmicroarraygene expressionmultiple hypothesis testinglinear mixed effects model Abstract Background: A limiting factor of cDNA microarray technology is the need for a substantial amount of RNA per labeling reaction. Thus, 20–200 micro-grams total RNA or 0.5–2 micro-grams poly (A) RNA is typically required for monitoring gene expression. In addition, gene expression profiles from large, heterogeneous cell populations provide complex patterns from which biological data for the targe