R help - Dec 2011 - minor allele frequency comparison

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.

Thanks
Scott

	[[alternative HTML version deleted]]

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