Improving identification of differentially expressed genes by integrative analysis of affymetrix and illumina arrays

Laura L. Elo, Mikko Katajamaa, Riikka Lund, Matej Orešič, Riitta Lahesmaa, Tero Aittokallio

Research output: Contribution to journalArticleScientificpeer-review

6 Citations (Scopus)


Together with the widely used Affymetrix microarrays, the recently introduced Illumina platform has become a cost-effective alternative for genome-wide studies. To efficiently use data from both array platforms, there is a pressing need for methods that allow systematic integration of multiple datasets, especially when the number of samples is small. To address these needs, we introduce a meta-analytic procedure for combining Affymetrix and Illumina data in the context of detecting differentially expressed genes between the platforms. We first investigate the effect of different expression change estimation procedures within the platforms on the agreement of the most differentially expressed genes. Using the best estimation methods, we then show the benefits of the integrative analysis in producing reproducible results across bootstrap samples. In particular, we demonstrate its biological relevance in identifying small but consistent changes during T helper 2 cell differentiation.
Original languageEnglish
Pages (from-to)369-380
JournalOMICS: A Journal of Integrative Biology
Issue number3
Publication statusPublished - 2006
MoE publication typeA1 Journal article-refereed


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