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Welcome to ArrayWiki.

Contents 1 Getting Started 2 Citing ArrayWiki 3 Statistics 4 Import Progress Meter 5 Microarray Technology Resources 6 Selected References 7 Help

[edit] Getting Started

1. You can search for experiments using the menu bar on the left.
2. Use the random page link to see sample experiment and chip detail pages.
3. View the Silver Medal List and ArrayWiki Exclusive experiments for very good examples of large datasets.
4. We have imported a large percentage of Affymetrix Datasets from GEO, simply type a GEO GSE ID into the search box to find out if an experiment of interest to you is already imported.
5. Read: Interpreting the BioPNG format.
6. Browse the Artifact Hall of Fame for some good examples of microarray artifacts.

BioPNG Source Code now available.

[edit] Citing ArrayWiki

Please cite the following two papers in publications referring to information or images obtained from this website:

Stokes T., Torrance, J.T., Li, H., Wang, M.D. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. BMC Bioinformatics, 2008 Jun; 9(Suppl 6):S18. paper Link

T. H. Stokes, R. A. Moffitt, J. H. Phan and M. D. Wang, chip artifact CORRECTion (caCORRECT): A Bioinformatics System for Quality Assurance of Genomics and Proteomics Array Data, Annals of Biomedical Engineering, 35 (2007), pp. 1068-1080. paper link tool link

[edit] Statistics

Imports

[edit] Import Progress Meter

Is there an experiment in GEO that you don't find in ArrayWiki?

Do you want to try your hand at importing it yourself?

Try our GEO Experiment Importer Tool. In 5 Easy Steps, you should be able to bring your experiment into ArrayWiki.

Database			Silver Medal List	Gold Medal List
	500	0	622	0	0
ArrayExpress	0	0	0	0	0
Celsius	0	0	0	0	0
ArrayWiki Exclusive	0	0	35	1	0

[edit] Microarray Technology Resources

• General information

1. Wikipedia Article describing microarrays.
2. Stanford's list of microarray resources
3. Affymetrix's information site
4. Brettschneider et al. article on microarray Quality Control
5. RMAexpress site

[edit] Selected References

1. T. H. Stokes, R. A. Moffitt, J. H. Phan and M. D. Wang, chip artifact CORRECTion (caCORRECT): A Bioinformatics System for Quality Assurance of Genomics and Proteomics Array Data, Annals of Biomedical Engineering, 35 (2007), pp. 1068-1080. paper link tool link
2. R. A. Irizarry et al., Multiple-laboratory comparison of microarray platforms, Nature Methods, 2 (2005), pp. 345-349. paper link
3. L. Shi, et al., The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements, Nat Biotechnol, 24 (2006), pp. 1151-61.
4. C. Li and W. H. Wong, Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection, Proceedings of the National Academy of Sciences, 98 (2001), pp. 31. paper link
5. Kluger, Relationship between gene co-expression and probe localization on microarray slides, BMC Genomics (2003). paper link
6. M. Suarez-Farinas, A. Haider and K. M. Wittkowski, "Harshlighting" small blemishes on microarrays, Bmc Bioinformatics, 6 paper link
7. L. Brodsky, A. Leontovich, M. Shtutman and E. Feinstein, Identification and handling of artifactual gene expression profiles emerging in microarray hybridization experiments, Nucleic Acids Research, 32 (2004). paper link

BioMIBLab

ArrayWiki was published in the BMC Bioinformatics Supplement:

Stokes T., Torrance, J.T., Li, H., Wang, M.D. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. BMC Bioinformatics, 2008 Jun; 9(Suppl 6):S18.

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[edit] Help

New to Wikis? Try this link for an introduction: Wikipedia Article (you can get this easily by typing 'wiki wiki' into Google)

If you're well-oriented, but still need reminders, download this helpful Image:Wiki-refcard.pdf.

Consult the User's Guide for in-depth information on using the wiki software.

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