[BioC] appropriate statistical test for post-array analysis

[r.athanasiadou]

Hi everyone,
I have used Nimblegen oligo arrays for ChIP-chip experiments.

I now have my results of which genomic regions are getting enriched in my
experiment.

I have calculated some values like GC-content of all the sequences on the
array and I would like to test if the distributions of these values remain
unchanged in the group of enriched sequences.

My intuition was the wilcoxon (Mann-Whitney) test but after discussing with
a colleague I really don t know if this is the best approach.

Additionally, if Wilcox.test is the correct approach, do I need to
pre-process the data? ie should I just put in the function the raw values of
every probe or should I first group them and put the frequencies for each
value in the function? I tried both approaches and they produce opposite
results.

I am worried that when I feed the raw values, there is a bias to accept the
alternative hypothesis because of the huge difference in the actual number
of values in the two groups.  


Could anyone point me to the correct statistical direction?

Finaly,what does the "location shift" that the Wilcox.test output refers to
mean? Is it the difference of medians?

Thank you
Niki