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Bioinformatics Advance Access published online on March 1, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm043
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Microarray Blob-Defect Removal Improves Array Analysis

Jun S. Song 1,{dagger}, Kaveh Maghsoudi 1,2,{dagger}, Wei Li 1, Edward Fox 3, John Quackenbush 1,4 and X. Shirley Liu 1,*

1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute; Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
2 Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA.
3 Microarray Core Facility, Dana-Farber Cancer Institute
4 Department of Cancer Biology, Dana-Farber Cancer Institute.

*To whom correspondence should be addressed. Dr. X. Shirley Liu, E-mail: xsliu{at}jimmy.harvard.edu, xliu{at}hsph.harvard.edu


  Abstract

Motivation: New generation Affymetrix oligonucleotide microarrays often have blob-like image defects that will require investigators to either repeat their hybridization assays or analyze their data with the defects left in place. We investigated the effect of analyzing a spike-in experiment on Affymetrix ENCODE tiling arrays in the presence of simulated blobs covering between 1 and 9% of the array area. Using two different ChIP-chip tiling array analysis programs (Affymetrix Tiling Array Software TAS and Model-based Analysis of Tiling arrays MAT), we found that even the smallest blob defects significantly decreased the sensitivity and increased the false discovery rate (FDR) of the spike-in target prediction.

Results: We introduced a new software tool, the Microarray Blob Remover (MBR), which allows rapid visualization, detection, and removal of various blob defects from the .CEL files of different types of Affymetrix microarrays. It is shown that using MBR significantly improves the sensitivity and FDR of a tiling array analysis compared to leaving the affected probes in the analysis.

Availability: The MBR software and the sample array .CEL files used in this paper are available at: http://liulab.dfci.harvard.edu/Software/MBR/MBR.htm

{dagger} These authors contributed equally.

Associate Editor: Dr. Joaquin Dopazo

Received on October 13, 2006; revised on January 21, 2007; accepted on February 3, 2007

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