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The difference between the array and RNA-Seq based gene lists could be due to the difference in platforms as well as in tissue samples used for expression profiling.
The only difference between the array and real-time detection was the positive signals observed for TC1507 event in some cases on array contrary to the results of the real-time detection.
Some of the inconsistency can be explained by the difference between the array platforms because only 3,758 out of the 5,107 genes were presented in the GSE2990 dataset.
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The high level of agreement in the observed CV and detection calls suggest any differences between the array versions at the probe-level are small.
This suggests that the disparity may arise through differences between the array and sequence technologies rather than noise specific to new sequencing technologies.
However, it is possible that pre-miRNA levels may not correlate with mature miRNA levels in the lung cancer setting, which might explain the observed differences between the array platform that targets mature miRNAs and the qPCR platform that targets pre-miRNAs.
The difference between array to array correlation within biological replicates (z = 2.73±0.38) and between non replicates (z = 1.90±0.35) indicates that there is a sufficiently high signal to noise ratio.
The new odd array is redefined as the difference between the existing array and the predicted one.
Due to scale differences between the arrays we also conducted global scale normalization across arrays.
The data was pre-processed to correct for systematic differences between the arrays.
Quantile normalization was performed including all arrays, to correct for large overall expression differences between the arrays.
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