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
using their .CEL files. Removal of the affected probes in the
MBR was shown to significantly improve sensitivity and FDR compared to
the affected probes in the analysis.
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)
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