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On the (lack of) ro...
On the (lack of) robustness of gene expression data clustering
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- Gamalielsson, Jonas (författare)
- Högskolan i Skövde,Institutionen för kommunikation och information
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- Olsson, Björn, 1962- (författare)
- Högskolan i Skövde,Forskningscentrum för Systembiologi,Institutionen för kommunikation och information
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(creator_code:org_t)
- World Scientific and Engineering Academy and Society, 2004
- 2004
- Engelska.
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Ingår i: WSEAS Transactions on Biology and Biomedicine. - : World Scientific and Engineering Academy and Society. - 1109-9518 .- 2224-2902. ; 1:2, s. 198-204
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Abstract
Ämnesord
Stäng
- We assess the robustness of partitional clustering algorithms applied to gene expression data. A number of clusterings are made with identical parameter settings and input data using SOM and k-means algorithms, which both rely on random initialisation and may produce different clusterings with different seeds. We define a reproducibility index and use it to assess the algorithms. The index is based on the number of pairs of genes consistently clustered together in different clusterings. The effect of noise applied to the original data is also studied. Our results show a lack of robustness for both classes of algorithms, with slightly higher reproducibility for SOM than for k-means.
Ämnesord
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Nyckelord
- Bioinformatics
- Bioinformatik
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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