Question: Tumor subtype: nearest centroid classifier
gravatar for ddjima2014
2.1 years ago by
ddjima20140 wrote:

I have a signature genes similar to pam50 (breast cancer signature) from other tumor. How should I use "intrinsic.cluster" OR "intrinsic.cluster.predict()" function in genefu package to do nearest centroid classifier to assign the tumor subtype?

I have a matrix like this that define the subtype:

                Basal        Her2       LumA         LumB    Normal
IMAGE:84786  -5.04 -0.83372727 0.66759259 -0.284999992 -1.076800
IMAGE:725321 -3.30 -2.62460000 1.88457143 -0.863454546 -0.695600

I did intrinsic.cluster() with the 3 centroid with the signature genes, BUT I got cluster.1, cluster.2 and cluster.3. How do I associate this cluster to the centroid subtype in my signature genes?

Data used to do "intrinsic.cluster())

700 samples x 20000 genes expression as column
20000 genes x 3 column of annotation
Annotation of the 500 signature genes.

I don't know how to tell incorporate a predefined subtype I have ?

Appreciate your input?

rna-seq R genome • 969 views
ADD COMMENTlink modified 2.1 years ago by genomax68k • written 2.1 years ago by ddjima20140
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2062 users visited in the last hour