I'm currently using GEO2R to analyze a microarray data set. There is an option to generate the 250 most statistically significant genes, which calculates an adjusted p-value using the Benjamini-Hochberg method to control the false discovery rate.
My understanding of the Benjamini-Hochberg process is that you first calculate the p-values, then sort and rank the p-values. The smallest value gets a 1, the second 2, and the largest N. The p-values are multiplied by N and divided by its assigned rank.
My question is, is N the total number of genes (54715) or does GEO2R only calculate the Benjamini Hochberg adjusted p-value on the smallest 250 p-values?