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Picture of Patrik Edén

Patrik Edén

Senior Lecturer

Picture of Patrik Edén

Accounting for one-channel depletion improves missing value imputation in 2-dye microarray data

Author

  • Cecilia Ritz
  • Patrik Edén

Summary, in English

Abstract in Undetermined
Background: For 2-dye microarray platforms, some missing values may arise from an un-measurably low RNA expression in one channel only. Information of such "one-channel depletion" is so far not included in algorithms for imputation of missing values.

Results: Calculating the mean deviation between imputed values and duplicate controls in five datasets, we show that KNN-based imputation gives a systematic bias of the imputed expression values of one-channel depleted spots. Evaluating the correction of this bias by cross-validation showed that the mean square deviation between imputed values and duplicates were reduced up to 51%, depending on dataset.

Conclusion: By including more information in the imputation step, we more accurately estimate missing expression values.

Department/s

  • Computational Biology and Biological Physics

Publishing year

2008

Language

English

Publication/Series

BMC Genomics

Volume

9

Document type

Journal article

Publisher

BioMed Central (BMC)

Topic

  • Genetics

Status

Published

ISBN/ISSN/Other

  • ISSN: 1471-2164