Computational protocol: Diagnostic Value of Serum Angiogenesis Markers in Ovarian Cancer Using Multiplex Immunoassay

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Protocol publication

[…] Univariate data analysis including Shapiro-Wilk test, t-test and Mann-Whitney test were performed using Statistica software (version 12.0; StatSoft Inc., Tulsa, OK, USA). Comparison between studied groups were evaluated with t-test or Mann-Whitney test depending on the mode of distribution. p-values < 0.05 were considered to be statistically significant. Data distribution was tested with Shapiro-Wilk test. Univariate and multivariate receiver operating characteristic (ROC) curve and Partial-Least Squares Discriminant Analysis (PLS-DA) were calculated by MetaboAnalyst 3.0 web portal. For each analyte classical univariate (ROC) curve was evaluated to show graphical correlation between specificity and sensitivity. Moreover, for selection and classification of the most relevant features PLS-DA was applied. PLS-DA is a standard supervised chemometric analysis that uses multiple linear regression model to provide linear relations between multivariate measurements. Variable Importance in Projection (VIP) scores estimate the variable’s importance in the PLS-DA model []. The higher the VIP score, the more important is the studied variable in the classification. This method allowed us to select the most relevant angiogenesis factors in multimarker models. Multivariate receiver operating characteristic (ROC) curve based on support vector machines (SVM) was calculated for features with the highest discriminative ability. In order to make the data obtained by different techniques (ECLIA or Bioplex) comparable, it was pre-processed using the scaling option in Metaboanalyst web portal. […]

Pipeline specifications

Software tools Statistica, MetaboAnalyst
Application Miscellaneous
Organisms Homo sapiens
Diseases Neoplasms, Ovarian Neoplasms
Chemicals Osteopontin