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Figure 4 shows the percentage of isoforms that match UCSC human known genes, and the percentage of the matched ones that have correct fold change estimations (defined as estimated fold changes within the [-2,+2] range of their corresponding true fold changes).
The estimated fold changes in the suicide group were -1.51 for EMX2 and -2.16 for PLSCR4 relative to the non-suicide group.
However, the range of estimated fold changes varied, especially for the genes that were expressed in only one group (Fig. 1b- g).
This table is an extension of Table 2, and the estimated fold changes are the estimates of the exponentiated effect parameter.
Table 2 summarizes the estimated fold changes as the estimates of the exponentiated effect parameter, 95% confidence intervals, and p-values of these results, and Table 3 lists the same parameters for all significant interactions.
In Table 2 the estimated fold changes may be calculated as: γ percentage points, where the parameter y from column 8 is the estimate of the exponential e β of the estimated effect parameter β for diarrhoea in formula (1).
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The qPCR estimated fold change for MAT2A was below the cutoff of 1.5 (1.4 instead of 2.4).
This effect is most prominent when the estimated fold change based on all core probes is low (see Figure 5B and 5D).
The probe set normalization improved the performance of the methods based on ROC curves, but not necessarily estimated fold change.
In each case, the coefficient of the model represented the estimated fold change between infected and non-infected samples.
Estimated fold change for each comparison was calculated using ANOVA, and resulting t-statistics from each comparison were modified using an intensity-based empirical Bayes method (IBMT) [ 33].
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