Research output: Contribution to Journal/Magazine › Journal article › peer-review
Research output: Contribution to Journal/Magazine › Journal article › peer-review
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TY - JOUR
T1 - Near-optimal designs for dual-channel microarray studies.
AU - Wit, Ernst
AU - Khanin, Raya
AU - Nobile, Agostino
N1 - RAE_import_type : Journal article RAE_uoa_type : Statistics and Operational Research
PY - 2005/11/1
Y1 - 2005/11/1
N2 - Summary. Much biological and medical research employs microarray studies to monitor gene expression levels across a wide range of organisms and under many experimental conditions. Dual channel microarrays are a common platform and allow two samples to be measured simultaneously. A frequently used design uses a common reference sample to make conditions across different arrays comparable. Our aim is to formulate microarray experiments in the experimental design context and to use simulated annealing to search for near-optimal designs. We identify a subclass of designs, the so-called interwoven loop designs, that seems to have good optimality properties compared with the near-optimal designs that are found by simulated annealing. Commonly used reference designs and dye swap designs are shown to be highly inefficient.
AB - Summary. Much biological and medical research employs microarray studies to monitor gene expression levels across a wide range of organisms and under many experimental conditions. Dual channel microarrays are a common platform and allow two samples to be measured simultaneously. A frequently used design uses a common reference sample to make conditions across different arrays comparable. Our aim is to formulate microarray experiments in the experimental design context and to use simulated annealing to search for near-optimal designs. We identify a subclass of designs, the so-called interwoven loop designs, that seems to have good optimality properties compared with the near-optimal designs that are found by simulated annealing. Commonly used reference designs and dye swap designs are shown to be highly inefficient.
U2 - 10.1111/j.1467-9876.2005.00519.x
DO - 10.1111/j.1467-9876.2005.00519.x
M3 - Journal article
VL - 54
SP - 817
EP - 830
JO - Journal of the Royal Statistical Society: Series C (Applied Statistics)
JF - Journal of the Royal Statistical Society: Series C (Applied Statistics)
SN - 0035-9254
IS - 5
ER -