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

GONZÁLEZ GA; FRESNO C; MERINO G; LLERA A; PODHAJCER O; FERNÁNDEZ EA

Congreso; 3er Congreso Argentino de Bioinformática y Biología Computacional; 2012

Microarrays remain  the  most  accepted  tool in  transcri ptome studies  that require to analyze  a large  number ofsamples [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  líes on the  simultaneous evaluation of hundreds of arrays for quality control {QC) to discard, semi automatically, those  that do  not  meet  the  mínimum quality requirements. Currently,the most  used tools for quality control oftwo-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. lt facilitates global quality control allowing users to quickly  compare all arrays ata 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 comprehensiveanalysis.