Analysis of Affymetrix GeneChip® data using amplified RNA

Leslie Cope, Scott M. Hartman, Hinrich W.H. Göhlmann, Jay P. Tiesman, Rafael A. Irizarry

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


When small biological samples are collected by microdissection or other methods, amplification techniques are required to provide sufficient target for hybridization to expression arrays. One such technique is to perform two successive rounds of T7-based in vitro transcription. However, the use of random primers, required to regenerate cDNA from the first round of transcription, results in shortened copies of cDNA from which the 5′ end is missing. In this paper we describe an experiment designed to compare the quality of data obtained from labeling small RNA samples using the Affymetrix Two-Cycle Eukaryotic Target Labeling procedure to that of data obtained using the One-Cycle Eukaryotic Target Labeling protocol. We utilized different preprocessing algorithms to compare the data generated using both labeling methods and present a new algorithm that improves upon existing ones in this setting.

Original languageEnglish (US)
Pages (from-to)165-170
Number of pages6
Issue number2
StatePublished - Feb 2006

ASJC Scopus subject areas

  • Biotechnology
  • General Biochemistry, Genetics and Molecular Biology


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