[BioC] GCRMA

[cap2018@columbia.edu]

I have a set of microarray experiments to which I have applied both
the rma and gcrma preprocessing.  What I have read seemed to
indicate that the gcrma is better, however I am having issues with
p values resulting from my relevant comparison within the study.

There are 2 experimental factors, brain region and line. There are 6
chips in each group, 24 total (6 region1:line1, 6 region2.line1,
etc).  I applied a 2-way ANOVA resulting in p values for region,
line and their interaction.  When I make a frequency histogram of
the results for line (the most important comparison) for RMA, the
results look as expected with the largest number of pvalues close
to zero. When I make the same histogram for my GCRMA results, the
plot looks different, with the largest number of pvalues centered
around .2.  I wanted to apply statistical methods to figure out the
False Discovery Rate of the tests, but I'm not sure they are
relevant to these GCRMA results.

Any comments on GCRMA or FDR test would be helpful.

Thanks
Christine