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  • z1dane
    Junior Member
    • Jul 2009
    • 1
    #1

    Using DESeq to examine control variability

    Dear all,

    I have count data for 2 conditions, 10 normal samples (N) vs 10 diseased samples (D). When I compare for differential expression using DESeq and using conds (N, N, N, N, N, N, N, N, N, N, D, D, D, D, D, D, D, D, D, D), I get results such as higher expression in some normal samples and some diseased samples. I had hoped for expression patterns where it is either up or down in the diseased samples, but expression patterns were always mixed.

    So I was wondering about the variation among just normal samples and among diseased samples. Is it possible to use DESeq to test for differential expression in just normal/patient samples? How would I set the conds?

    Thank you in advance!

    z
    Tags: control, deseq, differential expression, disease, read counts
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