Agi4x44.2c: a two-colour Agilent 4x44 Quality Control R library for large microarray projects

GERMÁN GONZÁLEZ; CRISTOBAL FRESNO; GABRIELA MERINO; ANDREA LLERA; OSVALDO PODHAJCER; ELMER FERNANDEZ

Oro Verde

Congreso; Tercer Congreso Argentino de Bioinformática y Biología Computacional; 2012

Asociación Argentina de Bioinformática y Biología Computacional

Microarrays remain the most accepted tool in transcriptome studies that require to analyze a large number of samples [1,2] and in several prospective international efforts, in particular in cancer, that are currently running. One of the biggest challenges of these large-scale studies lies on the simultaneous evaluation of hundreds of arrays for quality control (QC) to discard, semi automatically, those that do not meet the minimum quality requirements. Currently, the most used tools for quality control of two-colour Agilent 4x44 microarrays are Feature Extraction (FE) [3] and QC Chart Tool [5], both developed by Agilent. FE creates a PDF report for each array containing several measures of quality, and then users must manually review each report to find problematic arrays resulting in a very time consuming task. On the other hand QC Chart Tool only shows line graphs for FE quality metrics, not allowing to explore intensities distribution, spatial patterns, etc. Here we present Agi4x44.2c, a new QC R library [4] that fulfills all mentioned limitations. It facilitates global quality control allowing users to quickly compare all arrays at a glance. Furthermore, unlike other Bioconductor packages (such as Agi4x44PreProcess [6] and arrayQualityMetrics [7]), Agi4x44.2c includes QC tools specific to the two-color Agilent 4x44 platform, for more complete and comprehensive analysis.