Opened 17 years ago
Closed 16 years ago
#10 closed task (fixed)
Analysis: Hierarchical clustering
Reported by: | Johan Enell | Owned by: | Jari Häkkinen |
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Priority: | critical | Milestone: | BASE 2.2 |
Component: | coreplugins | Version: | trunk |
Keywords: | Cc: |
Description
Hierarchical clustering, bottom-up.
The two closest points are merged and the new cluster is represented by an unweighted(median) or weighted(center of mass) average of the two points in gene expression space. This takes little RAM, allowing you to cluster a large number of genes, but the clustering results could be inferior to those obtained with e.g. average linkage. Also, clustering with absolute correlation as the distance metric does not work very well at all.
Change History (21)
comment:1 Changed 17 years ago by
Milestone: | → BASE 2.0 |
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comment:2 Changed 17 years ago by
Priority: | major → minor |
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comment:3 Changed 16 years ago by
Owner: | changed from Johan Enell to Jari Häkkinen |
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Status: | new → assigned |
comment:4 Changed 16 years ago by
Milestone: | BASE 2.0 → BASE 2.0+ |
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comment:5 Changed 16 years ago by
Milestone: | BASE 2.x+ → BASE 2.1 |
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comment:6 Changed 16 years ago by
Priority: | minor → blocker |
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comment:7 Changed 16 years ago by
Version: | → 2.0 |
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comment:8 Changed 16 years ago by
Milestone: | BASE 2.1 → BASE 2.0.1 |
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comment:9 Changed 16 years ago by
Milestone: | BASE 2.0.1 → BASE 2.1 |
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comment:10 Changed 16 years ago by
Priority: | blocker → critical |
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comment:11 Changed 16 years ago by
Milestone: | BASE 2.1 → BASE 2.2 |
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Version: | 2.0 → trunk |
comment:12 Changed 16 years ago by
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Resolution: | → fixed |
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Status: | assigned → closed |
Hierarchical clustering is now supported through MeV (http://www.tm4.org). This is the note regarding MeV:
MeV is now integrated as a Java Web Start application. It requires network and file access so it is signed. You must accept the certificate to be able to run MeV. All algorithms are avaiable for the user but they are currently not fully supported. The main objective was to get Hierarchical clustering working. The integration will be improved in upcoming releases.
Clustering support will be added through TM4s MeV software. Currently bioassay sets must be exported (support exists already in BASE 2.1) for clustering.