First, we investigated the associations between the incidence of HFMD and its pathogens and meteorological variables, using the HFMD data from between January 2010 and June 2013 (1276 data points), and then we conducted a prediction analysis using the HFMD data from between July 2013 and December 2014 (549 data points).
Further, we conducted a prediction analysis using the multinomial LASSO regression model implemented in the R library glmnet v1.1-4 (Frietmal et al. 2010).
We tried to assign 11 genetically heterogeneous cases of type AB into types A and B using the prediction analysis.
We next tried to design a predictor with a minimum number of CpG sites using the Prediction Analysis of Microarrays tool (PAM) [28].
Samples were labeled as normal, LMP, or stage III for class prediction using the Prediction Analysis of Microarray (PAM) classification algorithm, with separate training and test sample sets as recommended by Simon et al. [ 21].
The 30-gene set used to differentiate subtypes was determined using prediction analysis of microarrays (PAM) (Tibshirani et al, 2002), which was optimised by minimising the cross-validation training error (see Supplementary Table 2).
Classification of the Rembrandt samples was then performed using prediction analysis for microarrays using the signature gene class centroids [11].
Statistically significant changes in gene expression were identified using significance analysis of microarrays (SAM), and predictive genes were identified using prediction analysis for microarrays (PAM) [ 3].
Because the sample size used in this study is relatively small (N = 385), we estimated the effect of the total sample size on the accuracy of pigmentation prediction using a bootstrap analysis of the eye color data published previously (Liu et al. 2009), in which a AUC value of 0.91 was obtained for predicting blue eye color based on a large population sample (N = 6,168).
Expression microarray data were analyzed using hierarchical clustering and gene set enrichment analysis; differential gene expression was also determined by conditional permutation, and an age signature was derived using prediction analysis of microarrays.
