How do I calculate and subtract array background for customarray 4x2k?

Negative control probes are usually used to calculate background for subtraction. The area surrounding spots and no synthesis spots can not be used for background calculation because they give an over-estimation of background. In contrast to the 12K, users can not use the factory-built probes of the 4X2K because they are covered by attachment of the sectored hybridization cap and are inaccessible for hybridization.

Thus, users may need to provide their own set of negative controls. Alternatively, background from the lowest 1-5% of signal intensities on the array can be calculated. Please note that this approach may not work, if you optimize the array content in several iterations to select for probes with high hybridization signals.

In such situation, background subtraction step may be omitted, or add a set of negative controls. More.

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