Question: How to define Basal B subtype from TCGA breast cancer patient samples ?
gravatar for ZheFrench
15 months ago by
ZheFrench270 wrote:

TCGA provide a molecular classification (Luminal A , Luminal B, Basal, Normal like, HER2 enriched) Basal subtype can be divided in basal A and basal B. (Kao et al., 2009; Neve et al., 2006) It has been done using expression from MicroArray via Significance Analysis of Microarrays (SAM) or PAM using the nearest shrunken centroid methodology. I retrieved from the paper a gene list used to classify so I have some ideas to begin to work but I was wondering if there ware a more standard approach to do that using TPM gene expression values.

cancer tcga • 650 views
ADD COMMENTlink written 15 months ago by ZheFrench270

I would simply recommend clustering the samples using the gene signature that you have obtained. You could try the TPM values and also the scaled TPM values.

ADD REPLYlink written 15 months ago by Kevin Blighe51k

Yeah that was my first idea. By the way how do you scaled TPM values ?

ADD REPLYlink written 15 months ago by ZheFrench270

If you perform clustering using heatmap or heatmap.2 (in R), then just set scale=TRUE. Otherwise, you can scale your data to Z-scores with t(scale(t(MyData))), assuming that MyData has samples as columns and transcripts as rows.

Usually, people cluster, i.e., perform hierarchical clustering, the non-scaled data and then present the scaled data in the heatmap.

ADD REPLYlink written 15 months ago by Kevin Blighe51k
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