Opened 16 years ago

Closed 15 years ago

#10 closed task (fixed)

Analysis: Hierarchical clustering

Reported by: Johan Enell Owned by: Jari Häkkinen
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 16 years ago by Jari Häkkinen

Milestone: → BASE 2.0

comment:2 Changed 16 years ago by Nicklas Nordborg

Priority: major → minor

comment:3 Changed 15 years ago by Jari Häkkinen

Owner: changed from Johan Enell to Jari Häkkinen
Status: new → assigned

comment:4 Changed 15 years ago by Jari Häkkinen

Milestone: BASE 2.0 → BASE 2.0+

comment:5 Changed 15 years ago by Jari Häkkinen

Milestone: BASE 2.x+ → BASE 2.1

comment:6 Changed 15 years ago by Jari Häkkinen

Priority: minor → blocker

comment:7 Changed 15 years ago by Jari Häkkinen

Version: → 2.0

comment:8 Changed 15 years ago by Jari Häkkinen

Milestone: BASE 2.1 → BASE 2.0.1

comment:9 Changed 15 years ago by Jari Häkkinen

Milestone: BASE 2.0.1 → BASE 2.1

comment:10 Changed 15 years ago by Nicklas Nordborg

Priority: blocker → critical

comment:11 Changed 15 years ago by Jari Häkkinen

Milestone: BASE 2.1 → BASE 2.2
Version: 2.0 → trunk

comment:12 Changed 15 years ago by Jari Häkkinen

Clustering support will be added through TM4s MeV software. Currently bioassay sets must be exported (support exists already in BASE 2.1) for clustering.

comment:13 Changed 15 years ago by Jari Häkkinen

(In [3096]) Addresses #10, #352, #365. First checkin for JWS use to launch MeV.

comment:14 Changed 15 years ago by Nicklas Nordborg

(In [3098]) References #10: Hierarchical clustering

Added servlet for downloading bioassay set data in Mev format

comment:15 Changed 15 years ago by Jari Häkkinen

(In [3100]) Addresses #10 and #352. Now actually using the bioassayset used to trigger MeV.|

comment:16 Changed 15 years ago by Jari Häkkinen

(In [3101]) Addresses #10 and #352. Fixed problem with non-appearing tool icons in MeV.

comment:17 Changed 15 years ago by Jari Häkkinen

(In [3102]) Addresses #10 and #352. MeV jsp uses Servlet API to retrieve server information (name,port,...).

comment:18 Changed 15 years ago by Jari Häkkinen

(In [3105]) Addresses #10 and #352. MeV uses system tmp directory system properties.

comment:19 Changed 15 years ago by Jari Häkkinen

(In [3106]) Addresses #10 and #352. Removed hard coded indexes for datamatrix retrieval.

comment:20 Changed 15 years ago by Jari Häkkinen

(In [3110]) Addresses #10 and #352. Unique temporary filenames used at client side.

comment:21 Changed 15 years ago by Jari Häkkinen

Resolution: → fixed
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.

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