Hi,
We wish to do exon analysis on an existing RNA-seq dataset - we actually only need to do it for one gene. However, the only publicly accessible data is pre-normalised using a quantile normalisation. I know that this data would be unsuitable for DEXSeq (or DESeq/edgeR), but would it be valid to use limma voom on the data? I don't know what statistical assumptions voom makes.
Cheers,
Ian Sudbery
Quantile normalized counts? That sounds very strange. Or are they actually RPKM values? Please describe the pre-normalised expression quantities you have in more detail.