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  • honey
    Senior Member
    • Feb 2010
    • 151

    #1

    Question about gene expression array analysis

    My apology about a dumb question about old gene expression array:

    I have a custom array gene expression data with controls and Cancer as log transformed RMA normalized values. If I have to calculate fold chnage or difference in cancer and normal tissues -
    I will simply take difference of values cancer - normal and it will be log fold change and then if I want in linear scale I can take antilog of this difference.
    Could some one advice if I am thinking correctly or I am doing something wrong. Again my apology for this basic question.

    Thanks.
  • jiaco
    Member
    • May 2010
    • 35

    #2
    If you have log2 data and geneA is 8.0 in cancer and 6.0 in control, you have a 2.0 log2ratio (cancer-control). Which is 2^2 = 4 in fold change. But the ratio in (control-cancer) is -2 and 2^-2 is 0.25. If you prefer to see -4 in fold change, then use something like this (in R)

    a = log2ratio
    b = result (fold change)

    if(a<0){b=-1*(2^abs(a))}else{b=2^a}

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