Hi, I'm wondering if anyone ever calculated the CG contents for the probes in Infinium HumanMethylation450 BeadChip? Should they all be above 0.5? What I found out, however, is that none of them has CG content ratio above 0.5.
For example, the following is one cpg island probe, the CG content ratio is only 0.26 based on the fourth column (AAAACACTAACAATCTTATCCACATAAACCCTTAAATTTATCTCAAATTC). Am I doing the calculation the right way? Thank you very much for your help!!
*new edit: I think to put the question in a simpler way: is there any annotation file for HumanMethylation450 BeadChip array that could tell the CG content in each probe? The annotation file that I used for this question is obtained from: ftp://webdata2:firstname.lastname@example.org/downloads/ProductFiles/HumanMethylation450/HumanMethylation450_15017482_v1-2.csv.
cg00035864 cg00035864 31729416 AAAACACTAACAATCTTATCCACATAAACCCTTAAATTTATCTCAAATTC II AATCCAAAGATGATGGAGGAGTGCCCGCTCATGATGTGAAGTACCTGCTCAGCTGGAAAC[CG]AATTTGAGATAAATTCAAGGGTCTATGTGGACAAGACTGCTAGTGTCTCTCTCTGGATTG 37 Y 8553009 AGACACTAGCAGTCTTGTCCACATAGACCCTTGAATTTATCTCAAATTCG Y 8613009 F TTTY18 NR_001550 TSS1500