I've ran kallisto on my samples, and summarized the transcript level counts to gene level counts to perform a differential gene expression analysis. I'm also interested in differential transcript expression, which I will perform using Sleuth.
Exploratory analysis at the gene level revealed that a few of the samples were clustering by batch. Previously I've applied RUVg on my counts, but the counts were produced by featureCounts and the analysis was only at the gene level. I wanted to know if it's appropriate to use RUVSeq with counts produced from kallisto? I will very likely need to apply this at the transcript level as well. We would also have to create in silico empirical control genes (which are normally created by performing a DE analysis).
Otherwise are there any alternative methods I can use to remove unwanted variation for data produced by kallisto?