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If for some reason you wish to override that selection, then click the Change selection link and select the chip name in the drop-down menu or select New chip… if you would like to upload a different chip annotation (Figure 5).

In the Select coverage depth section, you can set the nominal read coverage depth for your array. This is by default set at 20 million reads. However, you can adjust this number for better accuracy or if you are evaluating low-expressing genes. If you are comparing the microarray data with a corresponding NGS dataset, you can use this option to scale your data to a more comparable order of magnitude. Take note that setting this to a higher number will result in longer computation times overall.

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The Sequence correction transform checkbox corrects intensity values for sequence-specific effects. It is turned off by default and we only advise that you select this option if there are wide differences in the GC content of your probes.

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