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Old 11-25-2010, 05:53 AM   #1
Location: UK

Join Date: Jul 2010
Posts: 10
Default Strange DE results


I am using DESeq to determine which genes are differentially expressed between my treated sample and control. I am looking at three different genotypes (G1,G2,G3), each exposed to two different treatments (T1,T2), plus a control (C). For each treatment/genotype (e.g. G1T1) combination I have three replicates (G1T1R1, G1T1R2...). I am testing for differential expression between treated and control for each genotype/treatment combination.

I am finding the results of the DE tests confusing. All of the DE genes in G1T1 are downregulated compared to controls, whereas most of the DE genes (~98%), in G2T1 are upregulated compared to controls. G3T1 in contrast, shows approximate equal numbers of up and downregulated genes. It seems possible to me that the first two patterns are a statistical artifact, and was wondering if anyone had some suggestions as to what could cause this? The volcano plots look symmetrical and the DE genes do not all lie close to the cut off curve.

Many thanks for any ideas,

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