Dear all,
I have a list of differentially expressed genes between 2 experimental conditions. I observed that one of the chromosomes (3 in mouse) has a lot more genes coming up as differential expressed, and I want to know whether this number is statistically significant.
I was thinking about using a permutation test in R or perl to randomly select differentially expressed genes for the whole pool of genes in the genome, and then check how many of these are located in chromosome 3, and compare these values against my obtained experimental values.
However, I'm a little lost whether this is a valid approach to solve my question, and also I don't know how to whether there are already algorithms out there doing this exact same thing.
Thanks!!