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【原创】Power/sample size analysis: step-by-step [精华]

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楼主 slisten
slisten
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这个帖子发布于9年零196天前，其中的信息可能已发生改变或有所发展。
I saw a lot of guys here raised questions on power/sample size analysis. Power/sample size is the priority issue of genetic association study. It's quite important but it's no so complicated as thought. Many software can handle this. The best one is nQuery Advisor. It's quite professional and powerful. But it's too expensive. So free small ones should be our favorite.

Too many free software can do power analysis. They all use the same or similar statistical models so their outcomes are also similar. Here I will introduce a software "PS: Power and Sample Size Calculation" as a example to briefly show how to calculate statistical power or sample size for association study. This software has several pros, such as small size, windows-based interface (most operations are based on mouse clicks), easily accessed help etc. Our lab has always been using this software for more than 5 years and published more than 10 association study publications. The reviewer don't care what software you use, they only care what the results stand for. I seldom use other software, but I think most of them are similar. The difference may only be the data input method and interface.

Home page: http://biostat.mc.vanderbilt.edu/wiki/Main/PowerSampleSize
Remember, if you use this software in your manuscript, you'd better cite the authors' publication(s). It's respect to the authors for their generousness and free distribution.

Let's start:
1) download and install the software. After the installation, program shortcut will appear in the Program menu.


2) Click the shortcut, you can see the software main interface.


3) Click the tag lag "Dichotomous", here is what we need for chi-square test. If you are running other test (e.g. T-test, regression etc), you can click other tags interested.


4) Choose what test you want, sample size or power

I use power as an example.

5) Choose whether your design is matched or independent


Then choose whether it's a case-control or prospective study


If you choose case-control, there will be two additional menus
One is to choose how your hypothesis express, odds-ratio or two proportions (MAF in case and control group)


Another is to choose whether your study is corrected, usually we select uncorrected chi-square because each cell is definitely larger than 5.


6) Then the population parameters input boxes show up. You can click each box's name (blue underlined character), the help document will appear to interpret what the parameters stand for.

7) Click "Calculate", the result will show up immediately. There is also a description on the power analysis in the bottom of the interface.


Finished...
Isn't it simple?
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2011-08-28 02:36 浏览 : 72218 回复 : 110
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slisten 编辑于 2011-12-24 11:59
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Just double your n because allelic association power analysis is based on allele count (2n) but not individual count (n).
2011-10-30 22:18
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oqpo
I have one more question. 还要请教slisten。
如果需要同时研究几个SNP位点与某疾病的关联，是否所有位点数据都分别带入计算？存不存在较正问题？
Yes, because different SNPs have different MAFs. But you don't have to list them all.
You can calculated the power based on the lowest MAF among SNPs and claim that your study group can provide higher power than this.
I don't think there's any adjustment for power calculation.
2011-11-05 09:56
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皇goo
slisten 您好
我现在已经得到了allele的 A/B，和genotype的 AA/ (AB+BB)，BB/(AA+AB)的OR值 我计算Power的时候到底是应该用哪个的OR值呢？

Allelic OR
2011-11-08 01:33
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