Correlation analysis, sample clustering analysis, and principal component analysis on all probes were performed to identify/exclude any possible outliers.
Multivariate analyses revealed sample clustering by season, with a relevant proportion of the variance explained by day length, temperature, salinity, phototrophic nanoflagellate abundance, chlorophyll a, and silicate concentration.
Subsequently, PCA was performed using the MPP software for both positive and negative ESI datasets to determine sample clustering and distinguishing ions (filtered by P < 0.05, adjusted for FDR between pre-dose and week 8).
Close sample clustering indicates their compositional similarity, whereas distant sample clustering suggests their diverse metabolomic compositions [17].
Unsupervised sample clustering (hierarchical clustering) and supervised sample classification (prediction analysis for microarrays [PAM]) was then performed.Differential protein expression (P < 0.05) was identified between SCA and IPMN (34/51 proteins, 67%) and between SCA and MCN (13/51 proteins, 25%).
In the 1996 data, the survey estimation procedure adjusted sample clustering as well as stratifying and weighted the data by household size.
But in the 2006 data, it only adjusted sample clustering and weighted the data by household size because sample stratifying information was not well documented.
The concern is that sample clustering may result, as many of the malware samples belong to the same malware family and often have similar file names.
Thus, sample clustering was related to microhabitat type (gardens or dumps) and not sample source (lab or field).
To examine patterns of sample clustering based on genetic similarity, we used the program STRUCTURE v. 2.3.1 [75].
However, the good sample clustering (Figures 2D and 2E) according to cell type and state using gene nRUD argues against that it is a major one.
