[BioC] Analyzing arrays with no replicates

[Sean Davis]

> 4. Once I have my filtered genes, how can I test for differential 
> expression among the 4 groups?  I've played around with mt.maxT (with the 
> test="f" option), but I haven't been able to get the proper class labels.

You won't be able to use any standard t-test.  A t-test requires you to have 
a standard deviation within each group.  In microarray analysis, almost all 
analyses are done only within gene, so since you have no replicates, you 
cannot do a t-test.  In fact, although limma would (I think) allow you do do 
such an analysis because it uses all the genes to determine a "pooled" 
standard deviation, I know that such an analysis will not pass any kind of 
peer review.  If you are using this for hypothesis generation, probably 
using fold-change is just as useful as hypothesis testing.  Others may 
correct me on this (and I would like to hear what others think), but your 
experimental design SERIOUSLY limits any statistics you attempt.

Sean