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]]

