Breast cancer AND RNA-seq data

[silviajserrano]

Hello All,
I have RNA-seq data from 60 breast cancer patients. I classified those tumors in molecular subtypes according to the expression of 6 IHC markers (ER, PgR, HER2, Ki67, EGFR, CK5/6) and now I would like to confirm the classification but using the RNA-seq data but I don’t know how to do it, someone can help me?

Silvia

[Richard Finney]

How do you think you would start?

What format is your data?

[silviajserrano]

Hello!
I have a file from each sample that contain: read counts, FPKM and TMP values. I started to analyze the differential expressed genes between molecular subtypes using RSEM. When I got the DE genes I did a heatmap to confirm that those DE genes define my subtypes but the problem is with the luminal A and B subtypes that in the heatmap are all mixed together.
I also try using the FPKM values from the genes included in the PAM50 and did the heatmap and I have the same problem so I think what I have to do first is to re-define my subtypes (specially luminals) before I start to do the DE analysis.

Silvia