Question: Tumor subtype: nearest centroid classifier
gravatar for ddjima2014
2.8 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 • 1.2k views
ADD COMMENTlink modified 2.8 years ago by genomax80k • written 2.8 years ago by ddjima20140
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