Prostate cancer data Sample Clauses

Prostate cancer data. The second data set is from a prostate cancer study (GEO GDS3289). It contains 99 samples, including 34 benign epithelium samples and 65 non-benign samples, with 20,000 genomic biomarkers. Missing values are present for 17,893 biomarkers, nearly 89% of all genomic biomarkers in this data set. In this analysis, we consider a binary outcome y, defined as y = 1 if it is a benign sample and y = 0 if otherwise, and test whether some genomic biomarkers are associated with the outcome. For the purpose of illustration, we choose three biomarkers (FAM178A, IMAGE:813259 and UGP2), for which the missing rates are 31.3%, 45.5% and 26.3%, respectively. We conduct a logistic regression of y on the three biomarkers. In this analysis, mi and mice packages give error messages and MICE-RF approach is computationally very expensive. Therefore, we only use our two proposed MI methods (MICE-XXXX and MICE-IURR) and the KNN-V and KNN-S methods in addition to the complete-case analysis. All 2107 biomarkers that do not have missing values are used to impute missing values in the three biomarkers.
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