[BioC] Patient and matched control paired data

[Steve [guest]]

I have a question about Paired analysis in EdgeR.  I have read the Users Guide (Aug 2013) and this clearly describes several types of paired analysis and how to build the appropriate design matrixes.  However, the design closest to my experiment (4.2, p40) doesn't seem to be a paired analysis.

My experiment is as follows: "cases" - placentas from patients with a well defined poor obstetric outcome, "controls" placentas from 20 subjects with good obstetric outcome.  The controls were selected from a large cohort (~4000) to be a close match to the cases.  Matching was based on ~20 characteristics (maternal age, BMI, gestational age, fetal sex, mode of delivery etc etc).  Hence there is 1 to 1 matching of cases and controls and hence a paired design.  We collected RNA-Seq data from all 40 - individually bar-codded, pooled and run on 3 lanes of a HiSeq2000.  

I am probably being a bit slow, but advice on what the design matrix should look like would be a real help.

Thanks.

Steve


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