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. 2012 Feb 27;7(2):e32394. doi: 10.1371/journal.pone.0032394

Figure 5. The Importance of loading cut-off for inclusion of probe set IDs in GO term annotation analysis.

Figure 5

The probe set IDs were sorted after loadings for the first principal component (GO:0043122 and GO:0007420) and second principal component (GO:0006695) following the PCA of the serum stimulation data (Figure 2). Overrepresentation analysis for the three terms was repeated for different cut-off values between 0.5% and 25% of probe set IDs with highest loadings. Shown are the resulting p-values. The vertical dotted line indicates the top 2.5% probe set IDs with highest loadings. This is the cut-off used in the text and as the default in the pcaInfoPlot function. The horizontal dotted line indicates the 0.05 significance level.