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As for the statistical power, the paired analysis of the same sample (n = 15 pairs) yielded a sizeable number of CpG sites with significant differential methylation after Bonferroni correction [ 9].
Study Design: The paired analysis of case patients with congenital abnormalities and matched population control subjects was performed in the population-based Hungarian Case-Control Surveillance of Congenital Abnormalities between 1980 and 1996.
Changes in the ratio between polysomal vs total RNA levels between 3T3-tTA and 3T3-tTA-eIF4E induced cells were identified using the paired analysis described above.
Microarray experiments were performed on total RNA from uninduced (+tet for 5 hr) versus induced (−tet for 5 hr) 3T3-tTA cells, and the obtained ratios were compared to the ratios of total RNA from uninduced (+tet for 5 hr) versus induced (−tet for 5 hr) 3T3-tTA-eIF4E cells using the paired analysis described above.
The paired analysis included the percentage difference from baseline for all control and CAP groups for each rat strain.
The linear regression slope coefficients in Table 1 indicate that the Z-statistic values using the paired analysis are higher than the unpaired Z-statistic values.
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In the second (paired) analysis, normal and subtyped tumor samples from the same patient were compared, allowing for more rigorously matched comparisons but limited by smaller sample numbers.
Lastly, we performed the same paired analysis between tumor primary culture and parental tissue using Partek Genomics Suite software, which allows to choose between two alternative CN algorithms.
The same paired analysis was performed using Partek Genomics Suite software (Partek Inc., St Louis, MO, USA), starting from CEL intensity files and applying the two alternative algorithms Hidden Markov Model (HMM, the same used by CNAG) and Genomic Segmentation (GS).
The median titres of anti-CCP in nonresponders were apparently higher at 12 months compared with baseline, but the individual paired analysis suggested a 4% decrease for each individual patient.
We plotted the average of each paired analysis against the difference for the same pair (central laboratory value − POCT value).
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