Accounting for one-channel depletion improves missing value imputation in 2-dye microarray data
(2008) In BMC Genomics 9.- Abstract
- 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... (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:
https://lup.lub.lu.se/record/950090
- author
- Ritz, Cecilia LU and Edén, Patrik LU
- organization
- publishing date
- 2008
- type
- Contribution to journal
- publication status
- published
- subject
- in
- BMC Genomics
- volume
- 9
- publisher
- BioMed Central (BMC)
- external identifiers
-
- wos:000253987100001
- scopus:40549129023
- pmid:18205949
- 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
- 2016-04-01 13:40:02
- date last changed
- 2024-01-09 16:36:52
@article{c251ec29-1b30-418e-9f63-0ed99e57d143,
abstract = {{Abstract in Undetermined<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/>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/>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 (BMC)}},
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}},
doi = {{10.1186/1471-2164-9-25}},
volume = {{9}},
year = {{2008}},
}