Harshlight: a "corrective make-up" program for microarray chips

Mayte Suárez-Fariñas^*¹ , Maurizio Pellegrino^*¹ , Knut M Wittkowski² and Marcelo O Magnasco¹

¹Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Ave, Box 212, New York, NY 10021, USA

²General Clinical Research Center, The Rockefeller University, 1230 York Ave, Box 327, New York, NY 10021, USA

author email corresponding author email* Contributed equally

BMC Bioinformatics 2005, 6:294doi:10.1186/1471-2105-6-294


Published:	10 December 2005

Abstract

Background

Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar artifacts, which might affect subsequent analysis. Although all but the starkest blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs), few tools are available to help with the detection of those defects.

Results

We develop a novel tool, Harshlight, for the automatic detection and masking of blemishes in HDONA microarray chips. Harshlight uses a combination of statistic and image processing methods to identify three different types of defects: localized blemishes affecting a few probes, diffuse defects affecting larger areas, and extended defects which may invalidate an entire chip.

Conclusion

We demonstrate the use of Harshlight can materially improve analysis of HDONA chips, especially for experiments with subtle changes between samples. For the widely used MAS5 algorithm, we show that compact blemishes cause an average of 8 gene expression values per chip to change by more than 50%, two of them by more than twofold; our masking algorithm restores about two thirds of this damage. Large-scale artifacts are successfully detected and eliminated.