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By measuring the decay rate of the graph from an exponential curve fit, we observed that the change in array size was slower when compared with the reduction of transcriptional activity (λ = 0.026/h and λ = 0.063/h respectively).
Following each recording, the suction was released but the arrays were held in place to ensure no change in array placement for subsequent recordings with different modes.
In our dataset, the specific change in array signal for MIG1 had an adjusted p-value > 0.05 over the complete experimental range.
The change in array was due to the manufacturers stopping availability of HumanHap300 Duo Illumina BeadChip arrays, during the period the study was conducted.
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These changes in array design and sample preparation protocols present significant challenges in the application of existing analysis methods.
Using this method, small changes in array signal were assigned z-scores to represent our confidence that the observed change in signal reflected actual changes in mutation frequency as opposed to oligonucleotide noise or "background" viral genetic diversity.
Confidence intervals for fold changes in array analysis are determined by algorithms internal to dChip, as previously described[ 17].
The two genes marked N/A show marginally statistically significant changes in Array Subjects but very highly significant changes in the opposite direction in New Subjects.
In order to determine if the changes in array signal intensities reflect true copy number alterations, we selected three loci for FISH experiments.
Inspection of the TrGT database revealed most dinucleotide motif SSRs to be near but outside open reading frames (data not presented) and therefore unlikely to disrupt coding sequences with changes in array length.
More than 0.14 differences characterised single copy number change in all cells irrespective of ploidy, making it possible to identify single copy number changes in array-CGH.
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