Joint estimation of calibration and expression for high-density oligonucleotide arrays

Ann L Oberg, Douglas W. Mahoney, Karla V. Ballman, Terry M Therneau

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Motivation: The need for normalization in microarray experiments has been well documented in the literature. Currently, many analysis methods treat normalization and analysis as a series of steps, with summarized data carried forward to the next step. Results: We present a unified algorithm which incorporates normalization and class comparison in one analysis using probe level perfect match and mismatch data. The algorithm is based on calibration models common to most biological assays, and the resulting chip-specific parameters have a natural interpretation. We show that the algorithm fits into the statistical generalized linear models framework, describe a practical fitting strategy and present results of the algorithm applied to an example dataset as well as based on metrics used in affycomp. The algorithm ranks amongst the top third of the affycomp competitors, performing best in measures of bias.

Original languageEnglish (US)
Pages (from-to)2381-2387
Number of pages7
JournalBioinformatics
Volume22
Issue number19
DOIs
StatePublished - Oct 2006

Fingerprint

Oligonucleotides
Oligonucleotide Array Sequence Analysis
Calibration
Joints
Normalization
Model Calibration
Generalized Linear Model
Microarrays
Microarray
Biological Assay
Linear Models
Assays
Chip
Probe
Metric
Series
Experiment
Experiments

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computational Theory and Mathematics
  • Computer Science Applications

Cite this

Joint estimation of calibration and expression for high-density oligonucleotide arrays. / Oberg, Ann L; Mahoney, Douglas W.; Ballman, Karla V.; Therneau, Terry M.

In: Bioinformatics, Vol. 22, No. 19, 10.2006, p. 2381-2387.

Research output: Contribution to journalArticle

Oberg, Ann L ; Mahoney, Douglas W. ; Ballman, Karla V. ; Therneau, Terry M. / Joint estimation of calibration and expression for high-density oligonucleotide arrays. In: Bioinformatics. 2006 ; Vol. 22, No. 19. pp. 2381-2387.
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