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?

Please be informed that mapping of the probes to the GenCode mouse genome (release M19) has already been done by Manhong Dai from the MBNI group. The most recent version of these so-called Custom CDFs (i.e. v23) has just been released; see here and select one of the GenCode-based PdInfo (recommended) or CDF packages (GENCODEE: probes summerized at the exon level, GENCODET: at the transcript level, GENCODEG: at the gene level).

<<edit>> I just noticed that for this array *only* remapped CDF packages are available (and not a PdInfo package).