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

Ritz, Cecilia LU and Edén, Patrik LU (2008) In BMC Genomics 9.
Abstract (Swedish)
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.



... (More)
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. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
BMC Genomics
volume
9
publisher
BioMed Central
external identifiers
  • wos:000253987100001
  • scopus:40549129023
ISSN
1471-2164
DOI
10.1186/1471-2164-9-25
language
English
LU publication?
yes
id
c251ec29-1b30-418e-9f63-0ed99e57d143 (old id 950090)
date added to LUP
2008-01-24 11:17:23
date last changed
2017-01-01 05:48:05
@article{c251ec29-1b30-418e-9f63-0ed99e57d143,
  abstract     = {<b>Abstract in Undetermined</b><br/><br>
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. <br/><br>
<br/><br>
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. <br/><br>
<br/><br>
Conclusion: By including more information in the imputation step, we more accurately estimate missing expression values.},
  author       = {Ritz, Cecilia and Edén, Patrik},
  issn         = {1471-2164},
  language     = {eng},
  publisher    = {BioMed Central},
  series       = {BMC Genomics},
  title        = {Accounting for one-channel depletion improves missing value imputation in 2-dye microarray data},
  url          = {http://dx.doi.org/10.1186/1471-2164-9-25},
  volume       = {9},
  year         = {2008},
}