Dear colleagues,
I would like to perform mutual exclusivity test on some expression data. My data are presented in form of contingency table, where columns are patients, rows are genes and "0"/"1" states if the expression of particular gene was favorable on disease recurrence in particular patient. Mutual exclusivity I mean any test that allow to check if genes and their expression rather act in concert or are mutually exclusive (if the effect of those genes is cumulative or not). I saw a lot of algorithms that are probable to perform such analyses, however they are all based on mutational data, not expression like mine (I mean algorithms like MEMo, RME, Dendrix and CoMEt). cBioPortal also performs it, however the analysis is restricted to data stored in cBioPortal and expression is normalized with z-score that doesn't in my field of interest.
I would appreciate any feedback, I don't mind using R/Python etc.
Thanks in advance!
Best regards
Dear Magdalena Orzechowska,
Look the link.s. May be useful.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266046/
https://arxiv.org/ftp/arxiv/papers/1604/1604.02099.pdf
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0700-7
Regards, Shafagat
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