minor allele frequency comparison
On Dec 9, 2011, at 2:44 AM, Scott Harding wrote:
Hi all, We are using two methods to identify SNPs. One is based on resequencing the genome and aligning the reads to the sequenced genome to identify SNPs (data available for 44 individuals). Another is based on SNP array with selected loci (30000 loci, 870 individuals). I want to compare the results from the resequencing based minor allele frequency and Array based minor allele frequency. What statistical test should I use? My table looks like Chromosome position Major/minor Resequencing SNP array chromosome 1 198432 C/T 75/13 1460/280 chromosome 1 14282752 A/G 69/19 1380/360 chromosome 1 595434 T/G 83/5 1680/60 I really appreciate any guidance.
You will get a much more knowledgeable audience about such questions (or at least the currently accepted strategies in your domain) when you post this on the Bioconductor mailing list.
Thanks Scott [[alternative HTML version deleted]]
I suspect they are also maintaining an HTML-free zone, but I don't know for sure. R-help at any rate is an HTML-free mailing list, but this post would get encapsulated in the archives in a strange little wrapper that requires extra clicking to navigate: https://stat.ethz.ch/pipermail/r-help/2011-December/298087.html
David Winsemius, MD West Hartford, CT