[BioC] Biological, technical or pooled replicates?
cei at sanger.ac.uk
Mon Nov 12 17:54:57 CET 2007
I would be very grateful for any suggestions or advise regarding the
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
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
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
pool (Male Mutant 1, Female Mutant 1) + pool (Male Mutant 1, Female
Mutant 2) + pool (Male Mutant 2 + Female Mutant 1)
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!
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