A proposed metric for assessing the measurement quality of individual microarrays.
BACKGROUND
High-density microarray technology is increasingly applied to study gene expression levels on a large scale. Microarray experiments rely on several critical steps that may introduce error and uncertainty in analyses. These steps include mRNA sample extraction, amplification and labeling, hybridization, and scanning. In some cases this may be manifested as systematic spatial variation on the surface of microarray in which expression measurements within an individual array may vary as a function of geographic position on the array surface.


RESULTS
We hypothesized that an index of the degree of spatiality of gene expression measurements associated with their physical geographic locations on an array could indicate the summary of the physical reliability of the microarray. We introduced a novel way to formulate this index using a statistical analysis tool. Our approach regressed gene expression intensity measurements on a polynomial response surface of the microarray's Cartesian coordinates. We demonstrated this method using a fixed model and presented results from real and simulated datasets.


CONCLUSIONS
We demonstrated the potential of such a quantitative metric for assessing the reliability of individual arrays. Moreover, we showed that this procedure can be incorporated into laboratory practice as a means to set quality control specifications and as a tool to determine whether an array has sufficient quality to be retained in terms of spatial correlation of gene expression measurements.
Kim
Kyoungmi
K
Department of Biostatistics, University of Alabama, Birmingham, Alabama, USA. kkim@ms.soph.aub.edu
Page
Grier P
GP
Beasley
T Mark
TM
Barnes
Stephen
S
Scheirer
Katherine E
KE
Allison
David B
DB
D000465:Algorithms; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D019544:Equipment Failure Analysis / Q000379:methods* / Q000592:standards*; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000592:standards; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000592:standards*; D011785:Quality Assurance, Health Care / Q000379:methods* / Q000592:standards*; D011786:Quality Control; D012015:Reference Standards