Biomedical Engineering Reference
In-Depth Information
23-k PRL (Ad-23k PRL) and 16-k PRL (Ad-16k PRL) were generated
to infect human umbilical vein endothelial cells (HUVECs) for 48 hours.
HUVECs infected with Ad-luciferase (Ad-Luc) were used as the control.
Gene expression proles were analyzed by using HG-u95Av2 gene arrays
(Aymetrix) containing 12,600 genes and ESTs. The numbers of replicates
were 2, 3, and 3, for the 23k PRL sample, the 16k PRL sample, and the
control sample, respectively.
3.2. Assessment of Array Data Quality
Data quality was examined using the 2D image plot for array comparability
between replicate arrays. Results indicated both the 16k PRL group and
the control group had one incomparable array with a coverage rate less than
80% (The results of the 16k PRL group are shown in Figure 4). Thus, data
analysis was performed with the exclusion of these two potential outlier
arrays.
Fig. 4. Assessment of array data quality. Examination of three arrays in the 16k PRL
group indicated the B array was not comparable to the other two arrays. Data patterns
between the B array versus the A and C arrays were widely spread with 1/3 data points
deviating away from the invariant band (constructed by two yellow curves). In contrast,
the band between the rst and third arrays was thinner with coverage rate 97% (coverage
rate is dened the proportion of genes within the yellow upper and lower boundary
curves). This observation indicates the experimental problem in the B array.
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