How to cluster TCGA data with a defined set of genes, in order to classify TCGA data?
I have a set of differentially expressed genes in from my analysis using melanoma cell lines from two melanoma sub-types which are independent of tumour stage and disease stage. Now I would like to see how my list of genes classify TCGA data?
The rationale behind this analysis is to understand if the set of genes identified from my in vitro analysis shows a same pattern in the in vivo data (TCGA). One method I could think of is taking the FPKM values of genes derived from my analysis, from the TCGA SKCM data (all the samples- Primary + metastatic) and then generating heat maps using hierarchical clustering.
Is my approach right? There are a few papers published recently which have used SOM based clustering which seems complicated to me.
Any help on this will be greatly appreciated. Thank you for your time.
