SNP statistics

invaderjim

Just wondering if anyone here has done any SNP genotyping? If so what kind of analysis did you use?
I have done some genotyping and now have to analyse the results, I'm pretty sure I should use a fishers exact test to compare my controls and disease groups but I'm not exactly sure how.
I am using graphpad to do the calculations, I thought I knew what I was doing but when I run numbers from papers that have done similar work I get a different answer for the p value than the one they have published, so I must be putting wrong values in somewhere!
If anyone has a worked example of a SNP calculation that would be great.

Thanks.

CramCycle

invaderjim wrote: »

I am using graphpad to do the calculations, I thought I knew what I was doing but when I run numbers from papers that have done similar work I get a different answer for the p value than the one they have published, so I must be putting wrong values in somewhere!

Not necessarily as the P value can change as more experiments are carried out. Can I ask what your p-value is and what the p-value in the papers you are looking at is?

Just to be clear, you will get a p-value equal to something whereas a paper will normally just tell you theat the aveerage was greater or less than a certain value, in most cases statistical significance is typically p<0.05 but if you can get it lower that that, it means it is even more likely not a fluke.

invaderjim

Hey CramCycle, cheers for replying to the post. It turned out that I had messed up the calculation. There looking better now, even managed to get some significant results (P<0.002).

CramCycle

invaderjim wrote: »

There looking better now, even managed to get some significant results (P<0.002).

Thats brilliant, sorry I didn't know to much about SNP stats themselves, just stats in general, if you ever get a chance, at sometime in the future, posting up a general work through for a sample calculation would be great.