ABSTRACT:

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

We introduce a new software tool, the Microarray Blob Remover (MBR), which allows rapid visualization, detection, and removal of blob defects of a variety of sizes and shapes from different types of microarrays using their .CEL files. Removal of the affected probes in the blob-defects using MBR was shown to significantly improve sensitivity and FDR compared to leaving the affected probes in the analysis.

DATA:

ENCODE ARRAY FILES (released Aug 8, 2006):
Full series of arrays  (GEO Accession number GSE5053)
Spike-in array (GEO Accession number GSM113413) and
corresponding Genomic Control Input array (GEO Accession number GSM113420)

SAMPLE SIMULATED FILES:
Single Blob-Defect of size p%  placed in 1 of 3x3 squares
1% Defect in Location 1,1
5% Defect in Location 1,3
9% Defect in Location 3,2