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  • hibari
    Junior Member
    • Sep 2016
    • 1
    #1

    edger and ccle

    Hi all,

    This is my first post here, so I am taking the opportunity to thank all the people who make this forum live.


    It is possible to find read counts from CCLE here :
    Office of Cancer Genomics
    https://ocg.cancer.gov/ctd2-data-project/translational-genomics-research-institute-quantified-cancer-cell-line-encyclopedia
    NCI's Office of Cancer Genomics (OCG) conducts structural, functional, and computational genomics research to improve patient diagnosis, treatments, and outcomes.


    I would like to use these data to find genes involved in resistance to treatment.
    I would like two group these cell lines in "sensitive" and "resistance" and test for the DEGs.
    However there is no technical replicats for these data.

    Let's say I have 32 cell lines in the "resistant" group and 32 cell lines in the "sensitive" group.
    Can I perform a DEG analysis with edgeR ?
    Can the 32 cell lines in each group be considered as replicats ?
    Do you think my approach is valid ?

    Thank you very much.
    Tags: ccle, edger
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