Hi all list, I want to annotate Illumina HumanHT-12 v3 chips by using the annotation file download from Illumina. The Illumina probes are classified by RefSeq NM Coding transcript, well-established annotation XM Coding transcript, provisional annotation NR Non-coding transcript, well-established annotation XR Non-coding transcript, provisional annotation Supplementary Content UniGene (Build 199) Experimentally confirmed mRNA sequences that align to EST clusters. I have the following questions 1) Should I use all kinds of these probes? Should I only use the RefSeq NM probes? 2) If different kinds of probes (such as RefSeq NM and RefSeq XM) are mapped to the same gene, how to combine them? Thanks. Feng [[alternative HTML version deleted]]