Is it possible to compare different array types (e.g., Mouse 430A and Mouse 430A 2.0) in GCOS?
GCOS cannot generate a comparison analysis between different array types. One can display Signal and Detection call data from arrays side-by-side in the pivot tab of GCOS. It is important to take into account the method of normalization or scaling when considering this type of comparison. As in any experimental design, it is essential to minimize experimental variation to allow focus on the biological differences. When samples are run on the same array type, the probe array type variable is removed. Results are most similar with samples run on the same array type. The Technical Note "Design and Performance of the GeneChip® Human Genome U133 Plus 2.0 and Human Genome U133A 2.0 Arrays" describes the performance of the new HG-U133 Plus 2.0 and HG-U133A 2.0 Arrays in comparison to the HG-U133A Array.