A comparison of background correction methods for two-colour microarrays
University of Ulster · Walter and Eliza Hall Institute of Medical Research · +3 more institutions
Abstract
MOTIVATION: Microarray data must be background corrected to remove the effects of non-specific binding or spatial heterogeneity across the array, but this practice typically causes other problems such as negative corrected intensities and high variability of low intensity log-ratios. Different estimators of background, and various model-based processing methods, are compared in this study in search of the best option for differential expression analyses of small microarray experiments. RESULTS: Using data where some independent truth in gene expression is known, eight different background correction alternatives are compared, in terms of precision and bias of the resulting gene expression measures, and in…
Citation impact
- FWCI
- 19.64
- Percentile
- 100%
- References
- 33
Authors
7- MEMatthew E. RitchieCorresponding
University of Ulster, Walter and Eliza Hall Institute of Medical Research, University of Cambridge, Peter MacCallum Cancer Centre, Royal Victoria Hospital
- JDJeremy D. Silver
University of Ulster, Walter and Eliza Hall Institute of Medical Research, University of Cambridge, Peter MacCallum Cancer Centre, Royal Victoria Hospital
- AOAlicia Oshlack
University of Ulster, Walter and Eliza Hall Institute of Medical Research, University of Cambridge, Peter MacCallum Cancer Centre, Royal Victoria Hospital
- MLMelissa L. Holmes
University of Ulster, Walter and Eliza Hall Institute of Medical Research, University of Cambridge, Peter MacCallum Cancer Centre, Royal Victoria Hospital
- DDDileepa Diyagama
University of Ulster, Walter and Eliza Hall Institute of Medical Research, University of Cambridge, Peter MacCallum Cancer Centre, Royal Victoria Hospital
Topics & keywords
- Bioconductor
- Estimator
- Gene chip analysis
- Computer science
- DNA microarray
- False discovery rate
- Offset (computer science)
- Statistics