[BioC] Intra variance Vs inter group variance: scared!

[Emmanuel Levy]

Dear All,

I've got two conditions and three replicates per condition:
A1 A2 A3 B1 B2 B3

To test the INTRA VS INTER group variance, I compared the fold changes
within group and between groups:

length(which(A1/A2 > 5))=686
length(which(A1/B1 > 5))=708

The fact that this is similar is quite scary! What do you think?

Do you know of a package that would show somehow that the noise found above
should not prevent me from getting meaningful results with these data?

Many thanks in advance for your help,

Emmanuel