Entering edit mode
10.5 years ago
muraved
▴
10
Hi everyone,
I am attempting to extract what I think should be the most basic information on SNP arrays from CEL files: intensity values for alleles A and B, and their respective genomic position, but no genotype calls or anything like that. I have attempted that using packages in Bioconductor (like affy and oligo), but I think I am overlooking something while getting stuck in all those fancy S4 class definitions.
The closest I have gotten to are the getA() and getM() functions in the oligoClasses package, and it appears the A() and B() methods do what I want, but I end up getting error messages like "!missing(alleles) is not TRUE".
I work HapMap affy100K and affy500K arrays, but I'd also like to have a more generic solution.
