Method Of P Value Adjustment For Multivate Test In R
1
1
Entering edit mode
8.7 years ago
J.F.Jiang ▴ 860

Hi All,

Here I came across a problem that I got a set of p values, e.g. 100 pvalues, but these p values are not independent

Then how can I do the pvalue adjustment for this set?

In R package, it seems that p.adjust is mainly developed for idependent hypothesises.

Thanks!

###############newly added (20th Feb 2013) Here is my situation, I just got a list of 100 p-values, some of which are associated.

For details, these 100 pvalues could be seperated into 7 groups, each group was calculated from a expression dataset. However, these datasets had 10%~60% overlap among each other, that is the pvalues inside a dataset were independent, but were not across the dataset, which bring the whole 100 p-values not independent.

So is there any solutions you know to directly and simply solve this? Some ref. pointed out to use the BH adjustment inside the R package, while choosing a loose criteria, e.g. 0.2, to define the significance level.

test r • 2.3k views
ADD COMMENT
4
Entering edit mode
ADD COMMENT
0
Entering edit mode

brilliant, thanks a lot

ADD REPLY
0
Entering edit mode

Hi David, actually, those methods in the website you offered are mainly discussed for GWAS data. Here is my situation, I just got a list of 100 p-values, some of which are associated.

For details, these 100 pvalues could be seperated into 7 groups, each group was calculated from a expression dataset. However, these datasets had 10%~60% overlap among each other, that is the pvalues inside a dataset were independent, but were not across the dataset, which bring the whole 100 p-values not independent.

So is there any solutions you know to directly and simply solve this? Some ref. pointed out to use the BH adjustment inside the R package, while choosing a loose criteria, e.g. 0.2, to define the significance level.

ADD REPLY

Login before adding your answer.

Traffic: 2329 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6