WHAT NEGATIVE CONTROLS CAN I USE FOR 4X2K CustomArray?
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 the12K, the 4x2K does not make available the factory-built probes because they are covered by the gasket of the sectored hybridization cap and are inaccessible for hybridization. Thus, users may need to provide their own set of negative controls. Alternatively, the background can be calculated from the lowest 1-5% of signal intensities on the 4X2K. This value may then be used for background subtraction. 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, the background subtraction step may be omitted, or a set of negative controls added.
