Analyzing Microarray Data Using WebArray
- 1 Department of Cancer Genetics, Sidney Kimmel Cancer Center, San Diego, CA 92121, USA
- 2 Department of Pathology & Laboratory Medicine, University of California, Irvine, CA 92697, USA
- 3 Genomics Core Facility, Sidney Kimmel Cancer Center, San Diego, CA 92121, USA
- ↵4Corresponding author (xqxia70{at}gmail.com)
INTRODUCTION
WebArray is a web platform for microarray data analysis. As an analysis suite designed by bench biologists, WebArray is user-friendly for life scientists without a bioinformatics background. It is simple to use but employs powerful analysis functions. Analysis is based on files uploaded by users. For Affymetrix GeneChip data, intensity files in CEL format can be used. For two-color experiments, WebArray can recognize intensity files generated from many different software packages. WebArray provides functions for data quality control, background correction, normalization, differential analysis, and plotting on a genome map. A user-friendly aspect of WebArray is the fact that users generally do not have to change the default parameters for common experimental designs, so they are usually protected from applying the wrong statistical tools. In most cases, novice users will have no problem finding explanations for file formats or terms in the extensive help system.
