although this may not be a question specifically for BioC, thought that I can still post it (if you do not mind), shall any packages for ChIP-seq analysis/statistical analysis be available to address it.
the question regards the statistical tests to show the specificity of phenomenon : let's consider an example - someone did a ChIP_seq for H3K27me3, and wants to show that a histone mark (eg H3K27me3 mark) increases on the genes involved in a particular biological process (eg 300 autophagy-related genes , from a total of 1000 genes with increased H3K27me3) after cell treatment .
what type of analysis would you recommend in order to show that the phenomenon (ie increase in H3K27me3) is specific to a set of genes (ie autophagy genes) :
-- taking random sets of non-autophagy genes (practically, the rest of the genes in the genome) -- and using parametric and non-parametric tests when comparing SET 1 (autophagy genes) with SET 2 (non-autophagy genes)
-- using hypergeometric / fisher-tests on a matrix (autophagy/no-autophagy genes vs increase/no-increase in H3K27me3) ?
thanks a lot, and happy weekend ;) !