[BioC] Biological, technical or pooled replicates?

[Cei Abreu-Goodger]

Hello all,

I would be very grateful for any suggestions or advise regarding the 
following.

We are about to run some Illumina Mouse-6 BeadChips. We want to compare 
a mutant vs wild type tissue. The problem is that we only have the 
following:
2 male mutant
2 female mutant
(and enough wild types of both genders)

Since the Illumina beadchips have 6 lanes, what would be the best 
combination(s) to set up?
Previously we have seen a rather strong "chip" effect, so ideally we 
would like to keep as much as possible on a single chip. We have also 
seen quite a strong gender effect.

Would something like the following be the best option?

2 male mutant + 1 female mutant
vs
2 male WT + 1 female WT

Or would pooling the male/female samples help to avoid the gender 
effect, since we're only interested in the mutant vs WT effect? Say 
something like:

pool (Male Mutant 1,  Female Mutant 1) + pool (Male Mutant 1, Female 
Mutant 2) + pool (Male Mutant 2 + Female Mutant 1)
vs
equivalent pools of wild types

The other option would be simply to have 1 technical replicate for the 
mutants and test each gender in a separate chip, but I don't believe 
technical replicates are the best option.

Again, any suggestions are more than welcome... Thanks!

Cei



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