I have been using the R package illuminaHumanv4.db to annotate our HT12 v4 array probes, and I have two questions:
* The description of the package says the data is assembled from public repositories. However, the reference manual notes that extensive reannotation has been carried out for the illumina probes. Am I right in thinking that the reannotation (ie genomic location, EnsemblReannotated ids etc) are from the paper:
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data
If not, can someone shed some light as to where this reannotation is coming from / citation of how it was redone?
* I am looking to map the probe IDs to ensembl transcript names, not just the gene names. The package doesn't have this information (only ensembl gene names). Could I obtain this somewhere? Perhaps information on the first point might help .. I know ensembl has these, but if the annotation differs, I can't go this route ..