When Should One Subtract Background Fluorescence in cDNA Microarrays?
Author InfoRobert Scharpf (Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics) Christine Iacobuzio-Donahue (Johns Hopkins University School of Medicine, Department of Pathology) Giovanni Parmigiani (Johns Hopkins University, Department of Oncology and Department of Biostatistics) Abstract Complementary DNA (cDNA) microarrays are a powerful tool for genomic analysis, but have noise components that make inferences regarding gene expression inefficient and potentially misleading. Background fluorescence, whether attributable to non-specific binding or other sources, is an important component of noise. The decision to subtract background fluorescence from foreground signal has been controversial, with no clear criteria for determining circumstances that may favor, or disfavor, background correction. While it is generally accepted that subtracting background reduces bias but ncreases variance in the estimates of the ratios of interest,no formal analysis of the bias
