Treatment of missing values for multivariate statistical analysis of gel-based proteomics data

ROMINA PAOLA PEDRESCHI PLASENCIA, Maarten L.A.T.M. Hertog, Sebastien C. Carpentier, Jeroen Lammertyn, Johan Robben, Jean Paul Noben, Bart Panis, Rony Swennen, Bart M. Nicolai

Research output: Contribution to journalArticlepeer-review

49 Scopus citations

Abstract

The presence of missing values in gel-based proteomics data represents a real challenge if an objective statistical analysis is pursued. Different methods to handle missing values were evaluated and their influence is discussed on the selection of important proteins through multivariate techniques. The evaluated methods consisted of directly dealing with them during the multivariate analysis with the nonlinear estimation by iterative partial least squares (NIPALS) algorithm or imputing them by using either k-nearest neighbor or Bayesian principal component analysis (BPCA) before carrying out the multivariate analysis. These techniques were applied to data obtained from gels stained with classical postrunning dyes and from DIGE gels. Before applying the multivariate techniques, the normality and homoscedasticity assumptions on which parametric tests are based on were tested in order to perform a sound statistical analysis. From the three tested methods to handle missing values in our datasets, BPCA imputation of missing values showed to be the most consistent method.

Original languageEnglish
Pages (from-to)1371-1383
Number of pages13
JournalProteomics
Volume8
Issue number7
DOIs
StatePublished - 1 Apr 2008

Keywords

  • DIGE
  • Missing value
  • Postrun staining
  • Preprocessing
  • Statistics

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