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

voom requires counts as input, in order to compute sensible log-CPM values and to fit a sensible mean-variance trend. So, if you don't have counts, then the best you can do would be to log-transform the data (if that hasn't already been done) and analyze those values as if they were microarray intensities with limma. See A: Differential expression of RNA-seq data using limma and voom() for details.

P.S. limma and voom should be separate tags, otherwise watchers of either tag won't get notified.