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
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