I previously used EasyRNASeq 1.8 to get count matrices from BAM files with a simple write.table command. I am trying to move to v. 2.0.8 but I just can’t seem to be able to do the same with the SummerizedExperiment object created… I know that I could create object sot feed directly to edgeR or deseq2 but we want to do our own analysis with various other techniques.
Probably a trivial thing but I am no R/Bioconductor wizard ;-)
Thanks in advance
Thanks for the input; I would have thought that loading easyRNASeq would have also loaded GenomicRanges... I'll insert the statement in my code.
easyRNASeq imports all the functions it needs from GenomicRanges, but doesn't depend on that package (e.g., it won't load it by default).