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  • Differential expression of miRNAs using edgeR

    Hi,
    I am working on elucidating pathologically relevant miRNAs responsible for disease progression and chemoresistance in chronic lymphocytic leukemia. For differential expression of miRNAs I am using the edgeR package. I am new to statistics, edger and any help would be highly appreciated. The samples are classified as 1) Indolent which has 7 patient samples 2) Chemo-responsive, 9 patient samples 3) Non-responsive, 7 patient samples 4) Control, 2 samples.
    I want to check the differential expression of miRNAs as follows:

    For comparing two groups like indolent vs chemo-responsive contrast matrix contrast(-1,1,0,0) works well. What should be the contrast matrix when comparing:

    (a) Control vs Indolent,Chemo-responsive,Non-responsive
    (b) Indolent vs Chemo-responsive,Non-responsive.

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