ArticleBMC medical genomics2012
Direct integration of intensity-level data from Affymetrix and Illumina microarrays improves statistical power for robust reanalysis.
Article in BMC medical genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 2 of them syntheses that pooled it.
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Who cites it
24 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Automated Hypothesis Generation to Identify Signals Relevant in the Development of Mammalian Cell and Tissue Bioprocesses, With Validation in a Retinal Culture System.Frontiers in bioengineering and biotechnology · 2020Article
- Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues.Scientific reports · 2019Article
- Development and characterisation of acquired radioresistant breast cancer cell lines.Radiation oncology (London, England) · 2019Article
- Molecular changes during extended neoadjuvant letrozole treatment of breast cancer: distinguishing acquired resistance from dormant tumours.Breast cancer research : BCR · 2019Article
- REDESIGN: RDF-based Differential Signaling Framework for Precision Medicine Analytics.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2018Article
- Comparative transcriptomic analysis of human placentae at term and preterm delivery.Biology of reproduction · 2018Article
- Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies.Scientific reports · 2016Article
- Antitumour activity of the novel flavonoid Oncamex in preclinical breast cancer models.British journal of cancer · 2016Article
- Observational
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6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAffymetrix GeneChips and Illumina BeadArrays are the most widely used commercial single channel gene expression microarrays. Public data repositories are an extremely valuable resource, providing array-derived gene expression measurements from many thousands of experiments. Unfortunately many of these studies are underpowered and it is desirable to improve power by combining data from more than one study; we sought to determine whether platform-specific bias precludes direct integration of probe intensity signals for combined reanalysis.
resultsUsing Affymetrix and Illumina data from the microarray quality control project, from our own clinical samples, and from additional publicly available datasets we evaluated several approaches to directly integrate intensity level expression data from the two platforms. After mapping probe sequences to Ensembl genes we demonstrate that, ComBat and cross platform normalisation (XPN), significantly outperform mean-centering and distance-weighted discrimination (DWD) in terms of minimising inter-platform variance. In particular we observed that DWD, a popular method used in a number of previous studies, removed systematic bias at the expense of genuine biological variability, potentially reducing legitimate biological differences from integrated datasets.
conclusionNormalised and batch-corrected intensity-level data from Affymetrix and Illumina microarrays can be directly combined to generate biologically meaningful results with improved statistical power for robust, integrated reanalysis.
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