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- Title
Surface Adjustment of Reverse Phase Protein Arrays using Positive Control Spots.
- Authors
Shannon Neeley, E.; Baggerly, Keith A.; Kornblau, Steven M.
- Abstract
Reverse phase protein arrays (RPPA) measure the relative expression levels of a protein in many samples simultaneously. Observed signal from these arrays is a combination of true signal, additive background, and multiplicative spatial effects. Background subtraction alone is not sufficient to remove all nonbiological trends from the data. We developed a surface adjustment that uses information from positive control spots to correct for spatial trends on the array beyond additive background. This method uses a generalized additive model to estimate a smoothed surface from positive controls. When positive controls are printed in a dilution series, a nested surface adjustment performs an intensity-based correction. When applicable, surface adjustment is able to remove spatial trends and increase within slide replicate agreement better than background subtraction alone as demonstrated on two sets of arrays. This work demonstrates the importance of including positive control spots on the array.
- Subjects
PROTEIN microarrays; CANCER genes; DNA microarrays; GENE expression; META-analysis
- Publication
Cancer Informatics, 2012, Issue 11, p77
- ISSN
1176-9351
- Publication type
Article
- DOI
10.4137/CIN.S9055