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ishasethi7 08-26-2015 02:12 PM

Finding differentially expressed genes between species
I have RNA Seq data from mouse and human skin ( 2 replicates each) and want to compare the expression of the orthologous genes to find any which are differentially expressed. I have quantile normalized the gene expression matrix across all 4 samples (2 mouse + 2 human). I eventually want to calculate the log fold change in expression of all orthologous genes between the 2 species. However before I do this, I should control for gene length, right? Will this be enough to give me an idea of the differentially expressed genes or should I be employing more sophisticated methods?

Can programs like DESeq be used for comparing gene expression between species?
Any comments would be helpful. Thanks a lot.

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