%0 Journal Article
%T Quality control in microarray assessment of gene expression in human airway epithelium
%A Tina Raman
%A Timothy P O'Connor
%A Neil R Hackett
%A Wei Wang
%A Ben-Gary Harvey
%A Marc A Attiyeh
%A David T Dang
%A Matthew Teater
%A Ronald G Crystal
%J BMC Genomics
%D 2009
%I BioMed Central
%R 10.1186/1471-2164-10-493
%X Of the 223 samples, all three criteria were assessed in 191; of these 184 (96.3%) passed all three criteria. For the remaining 32 samples, the RIN was not available, and only the other two criteria were used; of these 29 (90.6%) passed these two criteria. Correlation coefficients for pairwise comparisons of expression levels for 100 maintenance genes in which at least one array failed the QC criteria (average Pearson r = 0.90 ¡À 0.04) were significantly lower (p < 0.0001) than correlation coefficients for pairwise comparisons between arrays that passed the QC criteria (average Pearson r = 0.97 ¡À 0.01). Inter-array variability was significantly decreased (p < 0.0001) among samples passing the QC criteria compared with samples failing the QC criteria.Based on the aberrant maintenance gene data generated from samples failing the established QC criteria, we propose that the QC criteria outlined in this study can accurately distinguish high quality from low quality data, and can be used to delete poor quality microarray samples before proceeding to higher-order biological analyses and interpretation.The assessment of gene expression of the human transcriptome using microarray technology is a powerful tool for identifying genes and gene expression patterns involved in mechanisms of normal organ function and the pathogenesis of disease [1-3]. Microarray technology is ideal for studies of the human airway epithelium in health and disease in that the airway is one of the few internal organs where it is possible to repetitively sample sufficient quantities of pure populations of parenchymal cells from healthy individuals as well as individuals with lung disease [4-11]. In this regard, we and several other groups have used human gene expression microarrays to assess the expression of genes in the human airway epithelium, cell populations easily attainable via fiberoptic bronchoscopy [4,9,12-15].While it is easy to obtain the cells, the output from microarray data critically dep
%U http://www.biomedcentral.com/1471-2164/10/493