Detection and correction of probe-level artefacts on microarrays

BMC Bioinformatics

Tobias Petri¹  Evi Berchtold¹  Ralf Zimmer¹  Caroline C Friedel¹ 

[1] Institute for Informatics, Ludwig-Maximilians-Universität München, Munich 80333, Germany

关键词: Artefact detection;    Quality control;    Microarrays;   

Others  :  1088256
DOI  :  10.1186/1471-2105-13-114

 received in 2012-01-30, accepted in 2012-05-09,  发布年份 2012

【 摘 要 】

Background

A recent large-scale analysis of Gene Expression Omnibus (GEO) data found frequent evidence for spatial defects in a substantial fraction of Affymetrix microarrays in the GEO. Nevertheless, in contrast to quality assessment, artefact detection is not widely used in standard gene expression analysis pipelines. Furthermore, although approaches have been proposed to detect diverse types of spatial noise on arrays, the correction of these artefacts is mostly left to either summarization methods or the corresponding arrays are completely discarded.

Results

We show that state-of-the-art robust summarization procedures are vulnerable to artefacts on arrays and cannot appropriately correct for these. To address this problem, we present a simple approach to detect artefacts with high recall and precision, which we further improve by taking into account the spatial layout of arrays. Finally, we propose two correction methods for these artefacts that either substitute values of defective probes using probeset information or filter corrupted probes. We show that our approach can identify and correct defective probe measurements appropriately and outperforms existing tools.

Conclusions

While summarization is insufficient to correct for defective probes, this problem can be addressed in a straightforward way by the methods we present for identification and correction of defective probes. As these methods output CEL files with corrected probe values that serve as input to standard normalization and summarization procedures, they can be easily integrated into existing microarray analysis pipelines as an additional pre-processing step. An R package is freely available fromhttp://www.bio.ifi.lmu.de/artefact-correction webcite.

【 授权许可】

   
2012 Petri et al.; licensee BioMed Central Ltd.

【 图 表 】

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