Patrik Edén
Universitetslektor
Accounting for one-channel depletion improves missing value imputation in 2-dye microarray data
Författare
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.
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.
Avdelning/ar
- Beräkningsbiologi och biologisk fysik - Har omorganiserats
Publiceringsår
2008
Språk
Engelska
Publikation/Tidskrift/Serie
BMC Genomics
Volym
9
Dokumenttyp
Artikel i tidskrift
Förlag
BioMed Central (BMC)
Ämne
- Genetics
Status
Published
ISBN/ISSN/Övrigt
- ISSN: 1471-2164