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  • edgeR calculate CPM instead of lof2FC

    Dear, SEQanswer community,

    I want to detect differentially expressed genes between tumor and normal
    tissue, adjusting for any differences between the patients.
    I have 8 leukemia patients and 8 healthy donors.
    I follow the edgeR manual, particularly case study at chapter 4.1.

    I use the following commands:
    Code:
    > fit <- glmFit(counts, design)
    > lrt <- glmLRT(fit)
    > topTags(lrt)
    > colnames(design)
    > o <- order(lrt$table$PValue)
    > cpm(counts)[o[1:10],]
    This provides me top 10 CPM values for each of my sample. However, my goal is to get the log2FC for each sample.

    In what way I can calculate log2FC for each sample instead of CPM values in edgeR?

    Thank You very much for help!

    Olha
    Last edited by Olha; 02-10-2016, 03:10 PM. Reason: incorrect title

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