What is the best clustring method for gene expression base on logFC
1
0
Entering edit mode
4.9 years ago
Calangoa ▴ 30

Hello there, I have a small number of genes (about 40) containing there expression base on log transformation of fold change and their p.value for 12 individual microarray dataset. I decided to find co expression genes and cluster them to find similar datasets and co-expression. What clustering method is good for this data? previusly I wanted to do WGCNA but it is for a huge number of gene, then I decided to do heirecichal clustring but after reading different paper about clustring I found my self inexpert . what clustering method (average linkage, centeroid, complete, single linkage)and distance measurment (peardon, euclidean, manhattan,..)is better for my data?

I appreciate if anyone could help me.

clustring • 849 views
ADD COMMENT
1
Entering edit mode
4.9 years ago
ishackm ▴ 110

Hi Nafas,

For your data, I would recommend using hierarchical clustering (Dendrogram) to visually see the expression of the 40 genes between your samples, I would use the complete clustering method and the Euclidean measuring distance.

ADD COMMENT
0
Entering edit mode

Many Thanks ishackm.

ADD REPLY

Login before adding your answer.

Traffic: 1321 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