Microarray time-course clustering, using "hclust" in masigPro
1
0
Entering edit mode
@dimitrileonidlindenwald-7183
Last seen 5.8 years ago
Germany

Dear All, 

i have performed a time-course microarray experiment, found differentially expressed genes, and now intend to cluster those by their expression pattern over the time. 
maSigPro provides a way for hierarchical clustering via "hclust" method.

however the number of clusters that it forms is not deriven from the data but authomatically set to 9. It also is possible to define the number with "k". I thought the idea of hierarchical clustering is that the result is estimated from the data? 
Is there something that i miss? 

An alternative approach would be to use "kmeans" clustering with a k determined by a v-Fold Cross-Validation.
Are there any easy to use packages that could perform it, that you would suggest? 

 

 

clustering hclust maSigPro • 1.1k views
ADD COMMENT
0
Entering edit mode
efejiroe • 0
@efejiroe-9765
Last seen 5.6 years ago

Include "k=[your value]" in the functions input parameters in either masigpro wrapper function or see.genes function. Used it in the later case and it worked for me. Hope this helps.

ADD COMMENT

Login before adding your answer.

Traffic: 331 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6