i downloaded the clinical annotation file (Biotab format) for TCGA BRCA from the data matrix in order to look at Her2 copy number measured by FISH (something wich is done in clinical routine). I found the column with the annotation
The TCGA BCR Dictionary (https://tcga-data.nci.nih.gov/docs/dictionary/TCGA_BCR_DataDictionary_v2.3.xml) sais to this column: "Result of HER2 Copy Number testing (for the metastatic tumor), expressed as a range of values"
I am now confused because of 2 things:
1.) I do not see range of values, just one value
2.) i see many high values like 185. I cannot belive, that this is the copy number of Her2 (in clinics CN>6 is said to be positive).
Question: am i looking at the right column to find out the CN of Her2 measured by FISH?
Thank you for your help