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Sage-Bionetworks / CMSclassifier

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data preparation #2

Closed HaiHuaLiu closed 8 years ago

HaiHuaLiu commented 8 years ago

Hi,

Recently, I have read your paper published on NATURE MEDICINE. I am trying to use "CMSclassifier" to identify the molecular subtypes of colorectal cancer. Since the package requires the data frame of gene expression profile as the input. However, I just got the transcript level expression profile, what should I do to deal with my data if I want to use your package to identify the molecular subtypes of colorectal cancer?

Thanks.

Haihua

brian-bot commented 8 years ago

The CMSclassifier was optimized for gene-level expression levels and not transcription level. One thing to try would be converting your expression levels to gene-level and assessing with those values.