title: Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method.
abstract: BACKGROUND
  Large biological data sets, such as expression profiles, benefit from reduction of random noise. Principal component (PC) analysis has been used for this purpose, but it tends to remove small features as well as random noise.
  
  
  RESULTS
  We interpreted the PCs as a mere signal-rich coordinate system and sorted the squared PC-coordinates of each row in descending order. The sorted squared PC-coordinates were compared with the distribution of the ordered squared random noise, and PC-coordinates for insignificant contributions were treated as random noise and nullified. The processed data were transformed back to the initial coordinates as noise-reduced data. To increase the sensitivity of signal capture and reduce the effects of stochastic noise, this procedure was applied to multiple small subsets of rows randomly sampled from a large data set, and the results corresponding to each row of the data set from multiple subsets were averaged. We call this procedure Row-specific, Sorted PRincipal component-guided Noise Reduction (RSPR-NR). Robust performance of RSPR-NR, measured by noise reduction and retention of small features, was demonstrated using simulated data sets. Furthermore, when applied to an actual expression profile data set, RSPR-NR preferentially increased the correlations between genes that share the same Gene Ontology terms, strongly suggesting reduction of random noise in the data set.
  
  
  CONCLUSIONS
  RSPR-NR is a robust random noise reduction method that retains small features well. It should be useful in improving the quality of large biological data sets.
authors.affiliation: Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, 1500 Gortner Ave., St. Paul, MN 55108, USA. jwfoley@stanford.edu
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Foley
authors.forename: Fumiaki
authors.initials: F
authors.lastname: Katagiri
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D025341:Principal Component Analysis / Q000379:methods*