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?