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Open Access Research article

An analysis of intra array repeats: the good, the bad and the non informative

Yedid Elbez1, Shlomit Farkash-Amar2 and Itamar Simon2*

Author Affiliations

1 Faculté des Sciences de la vie., Université Louis Pasteur 28 rue Goethe., 67083 Strasbourg cedex, France

2 Department of Molecular Biology, Hebrew University – Hadassah Medical School, Jerusalem 91120, Israel

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BMC Genomics 2006, 7:136  doi:10.1186/1471-2164-7-136

Published: 5 June 2006



On most common microarray platforms many genes are represented by multiple probes. Although this is quite common no one has systematically explored the concordance between probes mapped to the same gene.


Here we present an analysis of all the cases of multiple probe sets measuring the same gene on the Affymetrix U133a GeneChip and found that although in the majority of cases both measurements tend to agree there are a significant number of cases in which the two measurements differ from each other. In these cases the measurements can not be simply averaged but rather should be handled individually.


Our analysis allows us to provide a comprehensive list of the correlation between all pairs of probe sets that are mapped to the same gene and thus allows microarray users to sort out the cases that deserve further analysis. Comparison between the set of highly correlated pairs and the set of pairs that tend to differ from each other reveals potential factors that may affect it.