As well as being able to save programs, the Spectrum could in addition save the contents of arrays, the contents of the screen memory, and the contents of any defined range of memory addresses.
The content of an array may include specific targeted regions of the genome or the entire genome arrayed on a single glass slide.
In addition, array vendors generally provide flexibility in design such that the researcher can easily adapt the content of the array in order to increase the resolution in one or more regions relevant for their study ('custom designs').
The more speculative content of the array tends to introduce a lot of low intensity noise from probes designed to regions that may not be transcribed.
Reproducibility and between platforms comparability was assessed on the whole content of each array and on a subset of well-matched transcripts common to the three investigated platforms.
The base content of the array was clustered according to the published cluster file from the CHARGE consortium (30), while the custom content, comprising ∼25 000 variants, was manually assessed/clustered whenever GenTrain scores were <0.9.
Because the validation dataset is derived on a different microarray platform, expression values need to be mapped and normalized in a merged dataset to account for differences in batch and the information content of each array.
To compare the two microarray platforms, we compared the complete content of each array based on detection (Affymetrix MAS5 present (P) or marginal (M) flag calls) and detection + differential expression (1.3-fold change and t-test p-value <0.05).
Since high GC content is likely to produce a more stable bond between two DNA strands, it is not surprising that a higher GC content of the array probe would produce a stronger bond with a diverged sequence than would be seen at low GC content, with conserved GC regions contributing extra stability to the otherwise weak bond.
Furthermore, the shared content of the array is also misleading for the estimation of cassette gain/loss events, as shared cassettes do not necessarily represent an evolutionarily conserved trait, but can have different histories, as is suggested by the lack of conservation in gene order between the arrays as opposed to the relatively conserved organization of the surrounding genomic genes [ 19].
