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Low quality datasets were excluded from the analysis if they presented low levels of signal (that may indicate insufficient hybridization to the probes), evidence of missing genes, imputed data, datasets that are too small (<4 samples).
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Diplotypes were generated based on the 4 studied SNPs, missing genes were imputed.
Missing gene expression values were imputed unsupervised using the k-nearest neighbors method of Troyanskaya et al. [ 38].
Classification is handicapped by thousands of missing values, and hence, the mean expression value of the reference distribution was used to impute missing gene values (Troyanskaya et al., 2001).
Missing gene expression values in this data set were imputed unsupervised using the k-nearest neighbors method [37], reducing the number of genes from 7399 to 6707.
Overall, the dataset consists of 5878 genes on 73 experimental conditions, missing values imputed by the K-Nearest Neighbor (KNN) method (Troyanskaya et al., 2001).
Missing values were imputed with impute package [ 48].
c: 3 missing values imputed.
b: 31 missing values imputed.
6 QOLtdi: QOLtd with missing data imputed.
Missing values were imputed using KNN-impute in the MultiExperiment Viewer [72], [73].
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Justyna Jupowicz-Kozak
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