Cite as: Cold Spring Harb. Protoc.; 2009; doi:10.1101/pdb.prot5260

This Protocol
Right arrow Full Text
Right arrow Update/discuss this protocolDiscussion icon
Right arrow Alert me when this protocol is cited
Right arrow Alert me when comments are published
Right arrow Alert me if a correction is posted
Services
Right arrow Similar protocols in this database
Right arrow Alert me to new releases of protocols
Right arrow Save to Personal Folders
Right arrow Download to citation manager
Right arrow Printer-friendly versionPrinter-friendly version
Citing Articles
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Wang, Y.
Right arrow Articles by Xia, X.-Q.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Wang, Y.
Right arrow Articles by Xia, X.-Q.
Related Collections
Right arrow Bioinformatics/Genomics, general
Right arrow Computational Biology
Right arrow Genetics, general
Right arrow Genome Analysis
Right arrow Microarrays
Right arrow Microarrays, general
Right arrow Analysis of Microarrays
Right arrow Analysis of Microarrays, general
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati   Add to Twitter  
What's this?
BSN globe

protocolProtocol

Analyzing Microarray Data Using WebArray

Yipeng Wang1,2, Michael McClelland1, and Xiao-Qin Xia3,4

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati   Add to Twitter Twitter    What's this?