Using DESeq to examine control variability

[z1dane]

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