How to: Process CEL files with mixed chip type aliases

Process CEL files with mixed chip type aliases

Author: Henrik Bengtsson
Created on: 2011-02-23

When Affymetrix develops a new chip type it is often sending it to a small number of research groups labelled as an "Early Access" array. For instance, before the HT_HT-U133A chip type was officially released it had been available for testing under the alias U133AAofAv2 as well as HT_HT-U133A_EA. Depending on what is the current alias, CEL files for the same physical chip type may have different chip type labels in their file headers. Potentially this could cause issues while analyzing the data, because the some tools are conservative and assumes that the user has made a mistake if mixed chip type labels are detect in the same set of CEL files. Although aroma.affymetrix protects users for doing such mistakes, it still allows for analyzing CEL files with mixed chip type aliases. There is not need to modify the CEL files.

For instance, the following setup of data set 'MyDataSet' will consider all CEL files to be of chip type HT_HG-U133A regardless if the CEL file headers indicates chip type HT_HG-U133A, U133AAofAv2 or HT_HT-U133A_EA.

csR <- AffymetrixCelSet$byName("MyDataSet", chipType="HT_HG-U133A")