I'm using the mouse Clarium D array from affymetrix to compare the differentially expressed mRNAs and lncRNAs. However, the lncRNAs annotated in the array are from different databases, such as ensembl, noncode, vega and et.al. But I want to get a consensus annotation, like ensembl, because I want to combine the microarray data with Chip-Seq results. I want to identify the differentially expressed lncRNAs that are also regulated by my target transcription factor.

My problem is, Chip-Seq can provide a common identifier like ensembl, but the lncRNA annotations are from different database, making it impossible to compare the two sets.

I have one solution, that is to re-annotate the probes from the array, by mapping all the probes to the Gencode mouse genome assembly, and then get a common ensembl annotation. Is that feasible for the mouse Clarium D array? Could anybody give any suggestions?