[BioC] GCRMA Fold Change

[cap2018 at columbia.edu]

I have used GCRMA to process and normalize my chip results.  I had
sufficient N to use 2 way ANOVA to analyze my data and I have used
Baysiean statistics to determine significance levels.

I have quite a few probe sets that are considered statistically
significant by my analysis, but have a fold change close to 1,
indicating the level of transcript is not THAT different between 2
groups.  Most of the probe sets that fit this description have very
low expression value from the GCRMA analysis, 1-6.

I did not filter my results as expressed/not expressed before I did
the analysis because I have been told it is unnecessary, and I get
many significant results that are definitely are expressed, but I'd
like to apply some kind of filter to my statistical results.
Is there a way to determine which transcripts are unexpressed, a
specific threshold for example?  For instance, values 7< are
probing expressed transcripts?

Christine