I have what I thought was a relatively simple question, but I haven't been able to find a simple solution..
We have a gene which is relatively unknown and we would like to understand in which conditions/diseases it is differentially regulated using unbiased mining of GEO. We have done this manually for a number of datasets and come up with some very novel suggestions for processes in which our gene may be involved, but are keen to take a more systematic and efficient approach (with our limited R experience).
We were initially planning on downloading the GEO profile for gene x, extracting the values, running a t-test, then
Is there an existing package that does this, or is there a simple way to approach this (our attempts so far have been unsuccessful!)?