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Affy SNP-chip metadata - how to read the probe sequences?
I have Affymetrix SNP-chip (250 K genomic) data. For each gene there are 56 probes =7 "quartets" (windows)*AB*PMMM*SenseAS. The information in the accompagnying CDF/TXT file looks like
SNP_A-1780520 rs16994928 ggatagtgttgacctc[A/G]agtacaggtttcaaaa 496 // 47873735 // 47874230 0.0 0.11 0.0
ProbeSetID Chromosome Expr1002 PhysicalPosition AlleleA dbSNPRSID
SNP_A-1780520 20 47874178 47874178 A rs16994928
I need to intepret these meta-data in terms of the probe sequences. In particular, where in the ggatagtgttgacctc[A/G]agtacaggtttcaaaa string are the seven quartets and how does the MM probe difer from PM probe
1 Answer
- Anonymous1 decade agoFavorite Answer
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