Getting started with your own analysis on Microarray data:
You can analyze your microarray data with a variaty of open source or commercial software such as GenePattern and GeneSpring. GHTF provides data in standard format such as .CEL, .DAT and .CHP that can be imported to these software. Annotation files are also provided and can also be downloaded from Affymetrix website. Affymetrix also provides a free software called Transcriptome Analysis Console(TAC) that does both gene level and exon level differential analysis.
You can also use R packages such as affy and limma.
Integrated Bioinformatics Tools available for MicroArray data analysis:
HPC also provides UCI researcher with integrated tools for analysis and comprehension of biological data. R based Bioconductor and Matlab bioinforamtics toolbox that can do be used analyze both NGS and microarray data are available to all HPC users. A commercial software specifically designed for biologists to easily analyze high throughput data, CLCbio Genomic Workbench, is also available on HPC for GHTF users. See CLCbio manual for a detailed instruction on how to use CLCbio to analyze your NGS data and microarray data.