Question: TCGA mRNA expression data for Breast Cancer: negative expression values in overexpressed genes
gravatar for s.maxouri
2.9 years ago by
s.maxouri0 wrote:


I am working with TCGA gene expression data (microarray based) level 3 for breast cancer and I have seen that the majority of the expression values is negative, even in genes that are known to be overexpressed. From what I understand the expression values are calculated as the log ratio Cy5(sample)/Cy3(universal human reference), so all the genes that are overexpressed should be above 0.

Could anyone tell me what these negative values mean? Am I missing a normalization step?


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