I am working on a custom CDF: Brainarray HGU133Plus2_Hs_ENTREZG_v17.
I want to convert the probe names to Ensembl names. I have a few specific questions; if instead anyone prefers to explain the right way of doing that, I'd also be glad.
1) Just to get it staight : the ENTREZG does not mean that the CDF itself is in anyway specific to ENTREZ, is that correct? I prefer working in Ensembl, so can I safely use HGU133Plus2_Hs_ENSG_v17 from Brainarray's website?
When I go to Brainarray's website and download the "CDF Seq Map Desc" file (last column), I see lines like that :
Probe Set Name Chr Chr Strand Chr From Probe X Probe Y Affy Probe Set Name ENSG00000000003_at X - 99884769 1019 717 209109_s_at ENSG00000000003_at X - 99884536 1054 679 209108_at
2) Does "Affy Probe Set Name" (the last column) stand for the probe set names of the Brainarray custom cdf?
3) What does the "probe set name" (first column) mean? Are they simply Ensembl names (those that I need?).