I am currently performing a CNA-analysis on Illumina Infinium EPIC data. As I have genes of interest discovered through a separate RNA-seq analysis, I created g-ranges for these to study their CNA profile using conumee.
However, after successfully running
CNV.create_anno (i.e. creating a conumee annotation object) where each gene of interest is present/annotated. The following analysis results in NA-entries for some genes present in the annotation object (i.e. in the resulting conumee CNV analysis object, genes that should be present in the @detail segment have NA both for both ratio and probes).
This error is not related to things such as if the name of the annotated region is in ENS or HGNC format. Has anyone else encountered this error, and if so did you manage to figure out the cause?