Hi,

I would like to double check whether the the quasi-likelihood method, (glmQLFit and glmQLFTest), are correct to use when looking for genes which expression is affected by a selected polymorphism? I have a SNP of interest and run the glmQLFit which gave me nice logical results. However, the bioinformatician I talked to told me edgeR is not an appropriate tool for this sort of analysis. Is it so? And if the answer is yes- why not?

Thanks!

edgeR is suitable for most differential read count contexts. If your data generates differential read counts, then edgeR should be appropriate. If it doesn't, then it won't be.