[StATS]: More lessons learned the hard way (January 31, 2006).
The more I do, the more I realize how little I have thought about how to properly conduct a statistical analysis. One lesson I thought I had learned was that it costs next to nothing to store information electronically, but it can often save you a lot of time. But recently, I have relearned the value of this lesson.
In a study of microarrays of 11 different tissues, a researcher wanted to compare expression levels of a broad class of genes. I used a randomization test and then applied a Bonferroni correction. Since there were 11 tissues, there were 11*10/2 = 55 different pairwise comparisons. A simple approach is to take each p-value and multiply it by 55. Those p-values larger than 1.0 were set equal to 1.0.
The researcher then asked for the unadjusted p-values. That is a reasonable enough request. I could divide all the Bonferroni adjusted p-values by 55 to get back the unadjusted p-values, but what would I do about the p-values that I set equal to 1.0. They could represent a whole range of values, so I was stuck. I had to run the randomization tests a second time (it takes several hours of computer time). How much easier would it have been to store the unadjusted p-values as an intermediate result. It would cost almost nothing to store an additional 55 values.
Previous weblog entries on this topic:
This work is licensed under a Creative Commons Attribution 3.0 United States License. It was written by Steve Simon on 2006-01-31, edited by Steve Simon, and was last modified on 2010-04-01. Send feedback to ssimon at cmh dot edu or click on the email link at the top of the page. Category: Data management
This page was written by Steve Simon while working at Children's Mercy Hospital. Although I do not hold the copyright for this material, I am reproducing it here as a service, as it is no longer available on the Children's Mercy Hospital website. Need more information? I have a page with general help resources. You can also browse for pages similar to this one at
for pages similar to this one at with general help resources. You can also browse Children's Mercy Hospital website. Need more information? I have a page reproducing it here as a service, as it is no longer available on the Hospital. Although I do not hold the copyright for this material, I am This page was written by Steve Simon while working at Children's Mercy