A pitfall in series of microarrays: The position of probes affects the cross-correlation of gene expression profiles

Gábor Balázsi, Zoltán N. Oltvai

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Scopus citations

Abstract

Using Escherichia coli cDNA microarray slides and Affymetrix GeneChips, we study how the relative position of probes on microarrays affects the cross-correlation of gene expression profiles. We find that in cDNA arrays, every spot located within the same block is affected by a similar, experiment-specific bias. As a result, the cross-correlation between some gene expression profiles is significantly altered, depending on the similarity between these "block-dependent" biases through the series of cDNA microarray experiments. In addition, the position of probes within the blocks can also contribute to the measured gene expression. We outline the necessary steps to computationally identify and correct these biases.

Original languageEnglish (US)
Title of host publicationMicroarray Data Analysis
Subtitle of host publicationMethods and Applications
EditorsMichael J. Korenberg
Pages153-161
Number of pages9
DOIs
StatePublished - Mar 24 2007

Publication series

NameMethods in Molecular Biology
Volume377
ISSN (Print)1064-3745

Keywords

  • Bias
  • Block
  • Correction
  • Cross-correlation
  • Gene expression
  • Microarray
  • Position
  • Probe
  • Spot

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