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Old 07-31-2015, 11:56 AM   #1
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Default RNASeq study design with different species and tissues

I am in the process of sequencing transcriptomes for RNASeq/differential expression from 8 nonmodel invertebrate species, for 3 tissues * 3 biological replicates each. 4 of these species have a phenotype of interest and 4 do not. We know the phylogeny, and each of the 4 species with the phenotype evolved it independently (the other 4 species are for sister group comparison).

I want to investigate differential expression across these 8 species AND 3 tissues AND convergent evolution.

The research questions:
1) Is variation in expression more strongly attributed to species or tissue? For this, I think PCA in DESeq or MDS in edgeR will answer it?

2) Are patterns of expression more similar because of phylogeny (i.e. sister species have similar expression) or because those species have the same phenotype?

3) Is there statistically an interaction between these 2 questions, and how to account for it?

Thanks, I am a noob at RNASeq!
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