I am a BSc student and I have a research to study an association between a SNP and a disease,, my study design is case control ..
I am planning to study 2 SNPs
SNP 1 ,, MAF is 27% in case
SNP 2 ,, MAF is 8.89 in case
And I am using OSSE , online sample size estimator which needs the minor allele frequency in controls … can it be 0?? as in controls it should be normal sequence
If not 0 ….How can I now the minor allele frequency in controls ?
· By putting this information’s Iam getting very small size of case as for 13 only in 200 of controls .. ! can I increase the size of cases ?? or can you advice me to the best solution
· If you know another sample size estimator other that OSSE ,,, that can be better in calculation , I would be happy to know
Thank you
soma
Hi Soma,
in addiction to their good chocolates, swiss university have good calculation and genetics tools among this one (http://csg.sph.umich.edu/abecasis/cats/gas_power_calculator/) for power calculation.
fred
Well, you can try and get the allele frequency from Ensembl. Choose humans, enter rsID, then population genetics. Choose a population which is the closest, by ancestry, to your population and see the allele of interest frequency. This will give you an idea of the allele prevalence in controls. Then you can use this estimate for power calculation.
http://www.ensembl.org/index.html
wrt small sample sizes, 27% vs 0% is a very huge difference, so not surprisingly you get rather small Ns
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