Hi everybody,

I am doing differential gene expression analysis on 22 samples from 3 batches. I have the count matrix generated using summarizeOverlaps() function. The reference genome is mm10 from UCSC. I need the annotation in Ensemble to compare my results with the results from another person using the same dataset. Is there anyway I can use R to find the corresponding Ensemble IDs ?

Thanks

You would use the org.Mm.eg.db package and the select() function. See the AnnotationDbi vignette for examples.