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Bioinformatics Advance Access originally published online on May 27, 2004
Bioinformatics 2004 20(16):2778-2786; doi:10.1093/bioinformatics/bth327
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Bioinformatics vol. 20 issue 16 © Oxford University Press 2004; all rights reserved.

Faster cyclic loess: normalizing RNA arrays via linear models

Karla V. Ballman *, Diane E. Grill , Ann L. Oberg and Terry M. Therneau

Division of Biostatistics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA

Received on January 9, 2004; accepted on February 20, 2004
Advance Access Publication May 27, 2004

Motivation: Our goal was to develop a normalization technique that yields results similar to cyclic loess normalization and with speed comparable to quantile normalization.

Results: Fastlo yields normalized values similar to cyclic loess and quantile normalization and is fast; it is at least an order of magnitude faster than cyclic loess and approaches the speed of quantile normalization. Furthermore, fastlo is more versatile than both cyclic loess and quantile normalization because it is model-based.

Availability: The Splus/R function for fastlo normalization is available from the authors.

Contact: ballman{at}mayo.edu

* To whom correspondence should be addressed.


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