Suppose we are performing a gene expression experiment looking at the effect of a drug and we have found an interesting gene, geneX, that has a uncorrected T‐test p‐value of 10^−6. What is the corresponding Bonferroni adjusted p‐value if we started with 15,000 genes? Suppose I have a hypothesis that the drug affects genes in the glycolysis pathway (which geneX is a member of) and I will only consider those genes for hypothesis testing. What is the Bonferroni adjusted p‐value if there are 450 genes in the glycolysis pathway?
I have also computed the Benjamini‐Hochberg (BH) FDR correction for this experiment and it is 0.001 at the p‐value ≤ 10−6 threshold, when considering all 15,000 genes.Suppose that my hypothesis is correct and among the glycolysis pathway genes p‐values ≤ 10^−6 are 10 times more frequent the genome‐wide rate for all 15,000 genes.
What can you say about the BH FDR for the same threshold computed on the glycolysis restricted geneset.