ImmGen microarray gene expression data: Data Generation and Quality Control pipeline

Much of the gene expression profiles generated so far by the ImmGen project were obtained using hybridization to microarray supports. Preliminary tests and results supporting the choice of the Affymetrix 1.0 ST platform have been reported. Here, we will document the data generation pipeline adopted for the project, the quality control (QC) steps and the criteria for data exclusion, as well as some of the basic analysis guidelines used to analyze expression across ImmGen data. The criteria evolved with experience and with the profiling of substantial numbers of cell-types, and those described are those adopted as of Feb 2012. Data and QC metrics for all ImmGen datasets as of this date are listed in Table 1.