added a better description of how we generate the sample GO and why, and added a couple of variables that should make calculations further down easier
changed sizeClass to useGOSizeClass
tried adding noise to gsea
tried upping the number of noise genes to 2000, still doesn't behave as I expect
Merge branch 'hypothetical' of https://github.com/rmflight/ccPaperRev into hypothetical
trimming range on distribution
Merge branch 'hypothetical' of https://github.com/rmflight/ccPaperRev into hypothetical
tried uniform distribution, didn't help much

Examining possibility of independence and forcing proportion of genes into lower 50% of ranks.
added gseaProportion function. Unfortunately, this won't work, because we need the indeces to remain the same, and the value of the statistic to move, ie. to change the rank between samples.
first crack at independent terms using the same indices. Not exactly promising
got things finally working, in gseaProportion, but list still gives better results
trying to force it by making up anywhere from 1:7500, and down only the last 2500
added a new function for having different significant proportions different between the two samples
back to using 50% as cutoff, and checking that the gseaProportion function does what we think
using variable proportions between samples
check that this will work with transformed from p-value to signed data
added comment about final things to try before doing current method
added function that merges p-values using Fishers method
moved gseaSizeRange to the R/code file
added function in exports