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.
###############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.