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All the mutations detected by the microarray method were also confirmed by conventional DNA sequencing.
Seventeen measurements reported an increase in DNA methylation by the qPCR method that was not detected by the microarray method (approximately 15% false negative rate in the microarray experiment).
IPA analysis of the genes detected by the microarray method identified 35 canonical pathways (Fig. 1B) and numerous biofunctions (Supporting Table 1).
We found no evident methylation change in samples treated with furan for 4 weeks compared with control samples by the microarray method.
This method allowed identification of more than twice the number of canonical pathways determined by the microarray method and seven times more than by proteomics (Fig. 1B).
In Figure 4, we show the ratio of the expression level estimated by the abundance within the EST database method [ 22] to that measured by the microarray method [ 24, 25].
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While RNA-Seq faithfully captures the effects of smoking as determined by microarray, the microarray method is less discriminating in capturing the smoking-dependent expression determined by RNA-Seq, consistent with the higher sensitivity of the latter method.
Validation of the microarray method by qPCR was also performed by direct comparison of fold-changes obtained by the two methods only in the subset of samples analyzed by microarrays (n = 3 4 per group).
Therefore, large-scale transcriptomic analyses using the microarray method have been superseded by the RNA-Seq generated through application of the recently developed next-generation sequencing (NGS) method.
With over 200 cells measured by metaphase karyotype and 459 cells measured by the PS microarray method, we found that the per-cell accuracies of the methods are roughly in line.
A comparison of the genotype/subtype results obtained with the two methods is shown in the table 2. Seventy-four of the 78 samples previously tested by Versant™, were successfully genotyped by the liquid microarray method (74/78, 95%).
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