TY - GEN
T1 - Semiparametric RMA background-correction for oligonucleotide arrays
AU - Bebu, Ionut
AU - Seillier-Moiseiwitsch, Françoise
AU - Liu, Hongfang
PY - 2007
Y1 - 2007
N2 - Microarray technology has provided an opportunity to simultaneously monitor the expression levels of a large number of genes in response to intentional perturbations. A necessary step towards successful use of microarray technology is background correction which aims to remove noise. One of the most popular algorithms for background correction is the Robust Multichip Average (RMA) procedure which relies on an unjustified parametric assumption. In this paper we first check the fitness of the RMA model using a graphical approach and then propose a new background correction method based on a semiparametric RMA model (semi-RMA). Evaluation of the proposed approach based on spike-in data and MAQC (Microarray Quality Control project) data shows our semi-RMA model provides a better fit to microarray data than other approaches.
AB - Microarray technology has provided an opportunity to simultaneously monitor the expression levels of a large number of genes in response to intentional perturbations. A necessary step towards successful use of microarray technology is background correction which aims to remove noise. One of the most popular algorithms for background correction is the Robust Multichip Average (RMA) procedure which relies on an unjustified parametric assumption. In this paper we first check the fitness of the RMA model using a graphical approach and then propose a new background correction method based on a semiparametric RMA model (semi-RMA). Evaluation of the proposed approach based on spike-in data and MAQC (Microarray Quality Control project) data shows our semi-RMA model provides a better fit to microarray data than other approaches.
UR - http://www.scopus.com/inward/record.url?scp=47649083346&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=47649083346&partnerID=8YFLogxK
U2 - 10.1109/BIBE.2007.4375756
DO - 10.1109/BIBE.2007.4375756
M3 - Conference contribution
AN - SCOPUS:47649083346
SN - 1424415098
SN - 9781424415090
T3 - Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
SP - 1404
EP - 1408
BT - Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
T2 - 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
Y2 - 14 January 2007 through 17 January 2007
ER -