Hi everyone,

I am trying to retrieve SNP names for MM probes on the Affymetrix 500K SNP array (specifically, some of the HapMap samples). In oligo, there is a function called probeNames which gives back the names, however, it only does so for PM probes. Is there an analogous function for MM probes in oligo or any other package?

Also, I was under the impression that each SNP has a corresponding set of 40 probes (20 MM, 20 PM). However, when I view the data in R, it seems like most SNPs only have 12 PM probes and a much smaller proportion have 20. Is this correct or an indication that the data are not imported correctly? In total, I see 6,443,200 probes for the Nsp chip, which doesn't equal 40 x 262,264 SNPs.

Due to these problems, I am so far finding it, in general, difficult to explore the data using R.

Thanks for any help guys!
Stacey
       
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