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Old 05-26-2017, 03:12 AM   #1
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Join Date: May 2016
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Default Differential expression of miRNAs using edgeR

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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