Hi João
I'm studying the correlation of genes using RNAseq. I'm wondering if you know some literature that could help me in that direction.. In lack of better solutions, do you think non parametric things like spearman would do the job?
In the DESeq package, we provide a function to perform a variance stabilizing transformation, which then gives you the possibility to use standard statistical techniques that require homoskedasticity. However, I do not have much experience on how well this works in practice for applications such as your.
This is because calculating correlations per gene does not make much sense unless you have many samples, and there are not that many published RNA-Seq experiments with more than a few samples. Two of the very few such large-scale RNA-Seq studies are the eQTL papers by Montomery et al. [Nature 464 (2010) 773] and by Pickrell et al. [Nature 464 (2010) 768]. These papers in fact use Spearman correlations.
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