GeneTitan artifacts

Friday, September 10th, 2010 by hinrich

GeneTitan well array

Ben Bolstad has created a while ago a gallery of images that illustrates various artifacts that can be seen when generating microarray data using Affymetrix' cartridge arrays. The images are generated by running functions that are included in Ben's affyPLM package for R. For the most current version have a look at the BioConductor web site.

A little while ago, Affymetrix has launched the GeneTitan instrument which can process up to two 96-well plates per day. However, as the processing of the arrays is completely different from the cartridge arrays, different problems can occur. We can see gradients / edge effects across the plate, but we can also see effects within a single well array (see icon - this documents a problem with the CCD camera that takes a number of smaller individual images to create a final composite image of the whole array).

Maybe we should start documenting the GeneTitan specific artifacts that we observe? Of course, this could in turn help the producer to optimize the instrumentation.

Posted in Molecular Profiling