Is there an integrated way to analyse mutation data and protein expression data

Question

[ShirleyDai]

Hi, I have two types of data, say: 1) genome wide DNA mutation data by next-gen sequencing. 2) several protein expression data from the same sample by immunohistochemical analysis Is there a best way (suitable r package) to analyse these data?

Thanks

[Sean Davis]

Answers to these will help determine how best to approach the data analysis.

• What question do you want to answer with your data?
• Is the information from IHC quantitative, or just qualitative (present/absent)?

[ShirleyDai]

My hypothesis is the differences of mutation load exist between high expression marker and low expression marker. My IHC data was classified qualitatively as high or low.