MOTIVATION: High-throughput and high-resolution mass spectrometry instruments are increasingly used for disease classification and therapeutic guidance. However, the analysis of immense amount of data poses considerable challenges. We have therefore developed a novel method for dimensionality reduction and tested on a published ovarian high-resolution SELDI-TOF dataset. RESULTS: We have developed a four-step strategy for data preprocessing based on: (1) binning, (2) Kolmogorov-Smirnov test, (3) restriction of coefficient of variation and (4) wavelet analysis. Subsequently, support vector machines were used for classification. The developed method achieves an average sensitivity of 97.38% (sd = 0.0125) and an average specificity of 93.30% (sd = 0.0174) in 1000 independent k-fold cross-validations, where k = 2, ..., 10. AVAILABILITY: The software is available for academic and non-commercial institutions.
MOTIVATION: High-throughput and high-resolution mass spectrometry instruments are increasingly used for disease classification and therapeutic guidance. However, the analysis of immense amount of data poses considerable challenges. We have therefore developed a novel method for dimensionality reduction and tested on a published ovarian high-resolution SELDI-TOF dataset. RESULTS: We have developed a four-step strategy for data preprocessing based on: (1) binning, (2) Kolmogorov-Smirnov test, (3) restriction of coefficient of variation and (4) wavelet analysis. Subsequently, support vector machines were used for classification. The developed method achieves an average sensitivity of 97.38% (sd = 0.0125) and an average specificity of 93.30% (sd = 0.0174) in 1000 independent k-fold cross-validations, where k = 2, ..., 10. AVAILABILITY: The software is available for academic and non-commercial institutions.
Authors: Haydn Hoffman; Sunghoon I Lee; Jordan H Garst; Derek S Lu; Charles H Li; Daniel T Nagasawa; Nima Ghalehsari; Nima Jahanforouz; Mehrdad Razaghy; Marie Espinal; Amir Ghavamrezaii; Brian H Paak; Irene Wu; Majid Sarrafzadeh; Daniel C Lu Journal: J Clin Neurosci Date: 2015-06-23 Impact factor: 1.961
Authors: Wei Guan; Manshui Zhou; Christina Y Hampton; Benedict B Benigno; L Deette Walker; Alexander Gray; John F McDonald; Facundo M Fernández Journal: BMC Bioinformatics Date: 2009-08-22 Impact factor: 3.169